We had time to investigate this more and one important condition applies to our use case => Our 3d tilesets use flat projections. So in a way, fixing the new york tileset is not relevant - and it is not even feasible as that tileset is already projected to curved globe.
But good news is that this branch tackles the issue very well:
I wish your team could merge this to master! It is a very promising solution.
An idea: the projections branch has quite many complex changes to the code base. I have been wondering if map projection functionality could be added to SCENE3D mode without so many changes => just make the globe ellipsoid a flat surface and thats all?