Don't you love it when you spend all this time writing up a question and then immediately solve it? Managed to solve this by adding a new static variable to the Animation class, public static var getTimerOverride:Function = null;. When this function is not null, everywhere that getTimer() is called is replaced by a call to getTimerOverride(). Then during initialization I just apply a custom function to get the game timer provided from C++ and then it's good to go. Simple enough.
I'm working on integrating TweenMax into a Scaleform project and I need to change TweenMax so that it ticks based on the game timer passed in from C++. How would I go about setting something like this up? I implemented something similar to this in GTween by changing staticInit() to take in a MovieClip that the ticker shape gets added to, which also contains the game timer variable that is used in staticTick() instead of calling getTimer(). So far the only similarity in TweenMax is that it has a ticker:Shape, but I can't figure out what to do with it.