We do our warp for the projection map in C4D and get that all fitting perfect to the geometry in the world. Then we export a vertex warp pass. This is just a still that will change a flat 2d render to the shapes in the world. (or a movie if you have motion control objects in the real world you can match to)
Then go and get revision effects ReMap plug in for AE (its pretty cheap). This can sit as an effect in an adjustment layer above your 2D or rendered 3D footage in AE, with the vertex warp from C4d plugged in to the effect. This will warp any 2D render to your final shapes in the real world and you can turn it on and off to check stuff. You can use the vertex map as reference in AE for where the “seams” are in the real world (where columns edges are or where the mullions in windows are). Plus you can output the viewport in AE to your projectors live (assuming you have a gfx card that can do this). Any footage renderered in 3D that is already in perspective or warped for the world should sit above this adjustment layer in your comp.
A 3D package is great for getting your geometry right to match whatever you are mapping too but in the end what you are projecting is 2D so you have the choice of going C4d or AE or both for the content. The 3D aspect of your content (just content here, I’m not talking about the 3D stuff that matches the architecture) has nothing to do with the real geometry of real world objects. So don’t limit yourself to one or the other just because you are mapping. Think about content as though you are working on a flat surface and then start working on the depth aspect.
In fact you can get into trouble with doing stuff in 3D only and thinking this way because your projectors can’t actually focus on more than one plane at a time. So you can end up designing something really cool that you can’t really pull off (in this physical universe anyway).
The thing that makes projection mapping work is the changes in lighting and shadows that match the geometry of your real world objects – and that can be done in either 2D or 3D.
With this approach you don’t have bring in geometry to AE to put your 2d stuff on – the warp render does that for you.