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I wouldnt ever trust any of the sets to actually be what they say they are, so you are correct in assuming you need to use clrmamepro to rebuild your sets. you won’t ever get a complete set as there are always some roms that don’t work but if you’re getting a pi 3, you’ll likely get support for more sets with lr-mame2003 (which is the deafult libretro mame emulator) Performance on mame4all-pi might be a bit better but I think it may also just depend on what roms you are trying to play.
But just follow this page and you should get the majority of your stuff working:
https://github.com/retropie/retropie-setup/wiki/Managing-ROMs
and kudos to you for reading the documentation first before asking questions, most people dont.