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How does Soldier's Blaster (and similar cards) work when interacting with a character who is both an Autobot and a Decepticon?

Different faction means "does not share a faction identity." For a character which is both an Autobot and a Decepticon, "not sharing a faction identity" means NOT Autobot and NOT Decepticon. Currently, this leaves Mercenary as the only different faction.
Source: Wizards of the Coast (2020-06-10)    【Link to Ruling】
Tags: Soldier's Blaster, Factions
If I slap a Decepticon Head on Cerebros can I play a Scoundrel's Blaster on Fortress Maximus? His tiny Head stars count toward the total but we were told he has no effect on Fort Max when he starts the game...would his faction affect him while his ability doesn't?
Card requirements are inclusive, not exclusive. However, in this case, Cerebros' Head is not active on the battlefield, so it doesn't contribute its faction identity or traits to the character. So, a Decepticon Head of Cerebros doesn't let you play a Scoundrel's Blaster on Fortress Maximus.
Source: Wizards of the Coast (2020-06-10)    【Link to Ruling】
Tags: Fortress Maximus, Great War Veteran, Cerebros, City Commander
I play a Decepticon Leader Body with an Autobot Head. Can I equip Matrix of Leadership to this character? If yes, does the Matrix's 'While on a Leader' ability function?
Card requirements are inclusive, not exclusive. This character fulfils both the Autobot and Leader requirements on Matrix of Leadership, so you may play the card on the character and the 'While on a Leader' ability will function.
Source: Wizards of the Coast (2020-06-10)    【Link to Ruling】
Tags: Body, Head
Can a card target something even if it won't have an effect? For example, can Unconventional Flying Object target a Body mode character?

Cards try to do as much as they can. You can play Unconventional Flying Object even if you don't have a Spaceship and it will only accomplish putting the Action into your scrap. There are a handful of Upgrades like Crushing Treads that are restricted to play on say "Put only on a Tank." - you can't play that card unless you have the specific kind of character to put it on. After you successfully put it on the right kind of character, the game won't check anymore if the upgrade is valid, so the character can flip to Bot mode, stop being a Tank, and the Upgrade will stay on.

An important rule to remember: The active player chooses in which order to resolve simultaneously triggered abilities.
Source: Wizards of the Coast (2020-06-10)    【Link to Ruling】
Tags: Head, Body, Play
Can you clarify timing on when heads activate in regard to finishing a trigger that caused the Body to be KO'd? Examples: Does Decepticon Quake damage his own Head when he dies? Octone killing a Body and then his bounty triggers does this kill the Head when it is played?

A head's deploy ability is a triggered ability. When both players trigger an ability at the same time the active players abilities will complete before the defending player. A player may order their own simultaneous triggers how they wish. The player controlling Quake may order Quake's damage trigger and Quake's head's deploy trigger such that Quake's damage ability resolves first, and Quake's head second. If Octone's controller is the active player, they must use Octone's bounty trigger before the defending player resolves their heads deploy trigger. This answer is an update on the originally published answer in the Roundup

An important rule to remember: The game checks for a player controlling zero characters at all times. However, Head character's deploy ability includes the following: 'When that character is KO'ed, even if it was your last character, deploy this battlefield in bot mode.' This is why you don't lose if your last character, a Body with a head, gets KOed.
Source: Wizards of the Coast (2020-06-10)    【Link to Ruling】
Tags: Decepticon Quake, Ground Assault, Head, Body, KO
If a card with a 'When this battles' trigger (e.g.: Emergency Defense Field) is played on a character after the attacker is declared, will the "When this battles' ability work?
The trigger for all "when this attacks/defends/battles" is at the same time and happens only once as the attacker is declared and tapped. If you use a "when this battles" trigger on a character to then play a "when this battles" upgrade onto that character, the upgrade won't trigger as it's now too late in the attack for those effects to trigger.
Source: Wizards of the Coast (2020-06-10)    【Link to Ruling】
Tags: Emergency Defense Field, Triggers
Do you treat the Body and Head as 1 or 2 characters?
One character.
2023-11-03 Update: This has been further clarified in this ruling.
Source: Wizards of the Coast (2020-06-10)    【Link to Ruling】
Tags: Head, Body, Turbo Rules
How should Stratagems be treated when using a W5 pack in Turbo?

Treat it like a regular star card.
Source: Wizards of the Coast (2020-06-10)    【Link to Ruling】
Tags: Stratagem, Turbo Rules
If Soundblaster brings back Crystal of Power with his ability that attaches a black pip weapon, back from the scrap, to himself, when he attacks, is the Crystal of Power scrapped at the end of the battle?

Crystal of Power will stay on. The time when Crystal of Power checks for "When the upgraded character battles" was passed the moment Soundblaster tapped to attack. Crystal of Power will trigger the next time the character battles, either defending or attacking.
Source: Wizards of the Coast (2020-06-10)    【Link to Ruling】
Tags: Sergeant Soundblaster, Weapons • Arms Dealer
If a combiner combined and untapped. Would Lose the Initiative cancel the untap combiner effect?

A team of characters combining isn't actually untapping; the resulting Combiner character is entering the battlefield untapped (like all characters which enter the battlefield after the start of the game, unless another card or ability says otherwise).
Source: Wizards of the Coast (2020-06-10)    【Link to Ruling】
Tags: Lose the Initiative, Combiner
With Fort Max, the second Head counts towards the TEAM star total. Does it also count towards Fort Max's CHARACTER star count or is that just Max and Cerebros stars combined?

While Fortress Maximus is in play, he and Cerebros's stars make up the character's star count. The second Head is not counted.
Source: Wizards of the Coast (2020-06-10)    【Link to Ruling】
Tags: Fortress Maximus, Great War Veteran
On my starting team one of my characters is Quake with a Flintlock. Can I sideboard in Fortress Maximus if I also put Flintlock on him?

You can't play Fortress Maximus without also playing Cerebros, and vice versa. Since you can't put both in your sideboard because you're only allowed one character in your sideboard, you can't sideboard Fortress Maximus in any effective capacity.
Source: Wizards of the Coast (2020-06-10)    【Link to Ruling】
Tags: Fortress Maximus, Great War Veteran
If Optimus - Legendary Warrior attacks in bot-mode with less characters than your opponent and you choose to repair a character upgraded with Toolbox, will you repair 4 because there are two times, or is it just 3 because it is one time repairing?

It's repair 1 "then" repair 1. So Toolbox will change it to repair 2, then repair 2, for a total of 4.
Source: Wizards of the Coast (2020-06-10)    【Link to Ruling】
Tags: Optimus Prime, Legendary Warrior
In this scenario, the Stratagem Sky Shadow Sync is also in play. What exactly happens when you only have Sky Shadow (Tank) and Sky Shadow (Plane) as your last characters and both get KO'd at the same time?

If all your characters are KOed, and there is no other card text saying otherwise (like a head's deploy ability), you lose. Sky Shadow Sync doesn't include such text, so if Sky Shadow (Tank) and Sky Shadow (Plane) are your last characters and both get KO'd at the same time, you lose the game.
Source: Wizards of the Coast (2020-06-10)    【Link to Ruling】
Tags: Sky Shadow Sync
If I attack one part of an uncombined Sky Shadow, and a triggered ability KO's that part before flipping cards resulting in Sky Shadow combining, does the attack end? Or does the attack continue against the combined Sky Shadow?

The attack continues since "Combiner Mode" is mostly another mode like Alt or Bot mode. You just can't "flip" to combiner mode without another card telling you to. Going to combiner mode is a one-way operation. Note that Sky Shadow will be untapped because the process of combining creates an untapped character.
Source: Wizards of the Coast (2020-06-10)    【Link to Ruling】
Tags: Sky Shadow (Plane), Sky Shadow (Tank), Sky Shadow, Elite Warrior, Sky Shadow Sync
Are the cards placed under Skytread randomized or placed in a specific order?

The cards are face down and therefore randomized.
Source: Wizards of the Coast (2020-06-10)    【Link to Ruling】
Tags: Skytread (Plane), Special Ops • Soldier, Skytread (Tank), Special Ops • Soldier, Raider Skytread, Special Ops • Soldier