Thanks for the screenshot.
1. Your very first post seems to indicate that you're assuming each model needs its own sub-typed EM. That is actually not true. Any EM, sub-typed or not, can access any model within the same assembly. We generate the sub-typed EM to make it easy to use in terms of queries. Using your DomainModel as an example, you can easily access your Common model from Confirmation EM by using:
var mgr = new ConfirmationEntities();
whereas using the Common EM, you would probably query as follows:
var mgr = new CommonEntities();
Even using a generic EM would work:
var mgr = new EntityManager();
As you can see, the only difference is cleaner syntax. Having multiple EMs or just 1 EMs would not make any difference in this regard.
2. Your second post about the SecAppUser error seems to indicate that the type is defined under 2 different namespaces within the same assembly. This issue has been fixed in 6.0.8.
I hope I've understood and answered your questions and assumptions correctly. But if not, please feel free to clarify further.