How to have separated enabled modules in multisite based on Domain Access?
It's been a year or two since I have used the Domain Access module on a site, but I don't think this is possible.

Domain Access runs all of the affiliate sites out of the same database, so there is a single {system} table, which is where all of the module info it.  Essentially, the module provides some content access rules based on domain (ie, node_access() based controls), along some helpers for other site-specific tasks and integration with other modules.  In the end, though, you still have a single database which means you have a single site.