/opt/retropie/configs/n64/mupen64plus.cfg edits the standard mupen64plus emulator settings. At my level of expertise(or really a lack thereof) I am unsure how the cores are separated but the es_systems.cfg also lists editable extensions and I would presume if the mupen64plus.cfg doesn't also affect the libreto version, then this probably does.
@mankysteve I'm not sure where you read that but as an experiment I tried "Star Wars - Rogue Squadron (USA) (Rev A).n64" It runs with a lot of audio glitches and slowdown. I would not call it playable. I am using a Pi3 at stock settings and mupen64plus tested with all of the various plugins.
If you are determined to play it just mess around with the resolution and plug-ins using runcommand menu and see what feels best to you.