Engine modifications per project

So the project generator lets us add new, custom source files to the engine on a per-project basis. This is great.

But, if I change the core engine source, that change affects all of the projects. So if one of my projects requires that I make some modifications to TSShapeInstance, or AIPlayer, that change would affect all of my projects.

So, to get around that, you need a new T3D install for each project that needs engine mods, Just like in the TGE days.

Is there any way to modify the core engine sources per-project? Some compiler hackery or #ifdef or preprocessor or something similar that would do the job?