I'm currently designing a Generals Challenge mission and wanted to try and figure out if that's important, or if I risk breaking anything. I'm not certain at this point how the game knows to substitute in the faction the player is playing as, but I have a lot of scripting which changes the enemy general's behavior, build lists and dialogue (delivered via briefing text) depending on which faction the player is playing as.

Well , if you mean the GC_ Units , it means General Challenge and the Units have been used for the Campions in GLA2 and USA5 ...
Some Special units just for their own Mission .
I wonder why didn't they just add more CINE Units .
Maybe Because CINE ones are only in Intro and Cinematic moments but this GC ones are used in the whole Mission .

But if you mean something else I'm sorry I'm wrong

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Sorry, I meant the 'Patch "GC_"' button.

I see in the Generals Challenge maps it looks almost like there are waypoints which mark where the player's base is initially spawned, but I don't see anything in the scripts for these missions which makes reference to those waypoints.

Since what I'm working on is a Generals Challenge mission, I'm wondering how I need to approach the problem of starting the player off with the right HQ (etc) based on which team they're playing as.