The ability for a WIM file to contain multiple image has nothing to do with MDT of ConfigMgr, it's simply part of the WIM specification. Both ConfigMgr and MDT use the same toolset to create, manipulate and deploy images from WIMs: DISM. Also,
both tools use the same task sequence engine.
So, to directly answer your questions, nothing changes with regard to WIM or images between the tools.
Jason | http://blog.configmgrftw.com