This is easily done in LB, just edit the game and change the emulator for it.
Well yeah, Retrobat is based off EmulationStation which is built off of Libretro and it's limited to the systems it emulates. You have far more emulator flexibility with emulator choices in LB. Also, LB now has an option to download and install Retroarch and all of its cores for you.
Just import the file types you want to import, you don't want to just scan your folder, especially if you have all that extra crap in them instead of roms.
As I said above, import the files you need to import, the emulators only run 1 file. For example if you import a CD based system game such as Sega CD or Playstation chances are your games are in cue + bin format (often multiple bin files) all you want to import is the cue file. This is why your Dreamcast games are trying to launch the incorrect file and failing.