I'm not sure what you mean by clean up the topology. It will leave tris in the mesh in some places, see here:
http://meshmixer.com/help/faq.html
So it will export mixed quad/tri meshes if you started with quads. Basically it only changes the mesh in the places where you've dropped parts. I am working towards better quad handling.
The smoothing will more or less take care of seams, but actually the drop algorithm itself tries to get rid of noticeable seams (although only at the mesh level, if you subdivide seams might show up).
OBJ is the main format for now, it can export to a few others (DAE, STL, etc). I am hoping to have FBX support in the next release, which should make it easier to integrate w/ Maya,Max,Mudbox,etc.


