Does a stratagem changing the attack/defence of a character change the base values for the character?

No. For example, if Private Pteraxadon’s Binary Edgewing Scythe upgrade mode removes the base defense from a defending Windblade, Combiner Hunter, it would not remove the +1 from the Camien Toughness stratagem.

Source: Aequitas (2022-08-23)    【Link to Ruling】

Tags: Stratagem

I am playing Nightbird in alt mode. My opponent plays Brainstorm and 2 follow-up actions. I reveal a Secret Action to stop 1 of the follow-ups. Does my opponent still take 3 damage?

Yes. Even when cancelled by an action such as Infiltrate, Jam Signals, or Overrule, a card is still played and an effects that refer to cards, or number of cards, being played still occur. Another example would be Thundercracker, Mach Warrior's bot mode effect.

Source: Aequitas (2022-08-23)    【Link to Ruling】

Tags: Nightbird, Enigmatic Agent

How does Steamroll and Grimlock, Dinobot Leader's bot mode ability work when KO'ing an undamaged character with Safeguard?

Attempting to Steamroll into an undamaged character with three health, such as Slammer, Combat Drone, and Safeguard 3 (for example Medic's Protective Field) will first see the damage reduced to 3 damage, and then KO the defender. No additional attack damage would be available to be steamrolled into another enemy.

Source: Aequitas (2022-08-23)    【Link to Ruling】

Tags: Safeguard

Does the order of the scrap matter?

No.

Source: Aequitas (2022-08-23)    【Link to Ruling】

Tags: Deck

If I Steamroll into an Autobot and KO them, but my opponent reveals a Heroic Resolve; do I do any additional damage?

No - the Autobot was not in fact KO'd.

Source: Aequitas (2022-08-23)    【Link to Ruling】

Tags: Heroic Resolve