I don't use RetroPie, but the ROMs that are dumped are bog-standard, I always verify against the hashes from DAT-o-MATIC, and they play fine in my standalone mupen64plus and Retroarch installs, which would be the options RetroPi could build on for emulating N64.
If RetroPie didn't work with them, it'd not only be something people would be raging about en masse, it'd mean that they had to actively work to break something.