If I'm correct, currently Silverlight Package Catalog included to toolkit can only work with xaps.
Are you planning to modify it so it can use also dlls zips.
As I write before, dynamic loading of xaps is just a half of solution:
Xap1: include A.dll and B.dll
Xap2: include A.dll B.dll and C.dll
Common assemblies should be moved away from xap and load on demand if xap needs them.
Currently manual parsing of externalparts in xap AppManifest can solve the issue. BUT, external part syntax does not support cases when external assemblies have dependencies on other assemblies. So I think you should provide some new additional rules to
externalparts or provide new manifest syntax.