Hi ArenMook,
I have found some inspiration in UTFAtlasEditor where you can just use information about selected sprite UVs and recalculate all UV of 3dMesh to use specific part of atlas texture. This way the 3DMesh will display a part of Atlas material as own texture and thats it.
I think there is a possibility to get sprite UVs from NGUI Atlas and do the same.
I am new to Ngui (not a programmer) and just started to explore scripts. Will post some effects if it start to work.
Before I was doing all the atlases by my hand for 3D.
It could be nice to use the same workflow with NGUI Atlas for 3D Objects when you do a mixed 2D/3D app.