When you do "export without dependencies" the toolset can still fill up the regular override folder with stuff, the one that's in your docs folder under Bioware/packages/core/overrites/toolsetexport
Usually you just go in and delete everything its created there to keep from breaking your single player campaign... but if you've downloaded someone else's mod where they haven't been organizing everything into their own module's folder, and they've been using that common overrides folder, then parts from their modules may have been overwritten.
Take it as a lesson as to why you should keep the files your module depends on in its own folder hierarchy. For example, the core overrides for my module, being an AddIn, are under Bioware/Dragon Age/AddIns/myModuleName/core/overrides/toolsetexport
If two different modules modify the same core 2DA files, but those modified files are stored in different locations, the game will attempt to merge them automatically for you at run time. The files will stay separate so they can be edited independently, and there's a good chance your two separate modules can run without stepping on each others toes. Check out
the builder wiki's page or
this tutorial for more information on making your modules as compatible as possible.
As to your specific question, I've never heard of the manifest.xml needing to be merged before, nor of a way to do it.