ParaLLEl is a good foundation as it aims for accuracy but it’s in early stages and afaik the main author isn’t working on it much. So it will take a while until it gets when it needs to be. For now, it’s just not as compatible as the other two emulators (PJ64 and Mupen).
The Mupen RetroArch Core has it’s own problems compared to the standalone. Problem is, it lacks the updates that made hard to emulate games work really well. All games from Factor-5 and the later games from BOSS work in both PJ64 and Mupen standalones but not on the core. There are some other games that also have problems in the core but work fine on the standalone, from my own tests.
So basically, the current state isn’t great if you want to use RetroArch as your primary N64 emulator. However, there’s talk about merging the best parts of the two cores soon (ParaLLel+GlideN64) and focus on one core instead of two so that will hopefully change the deal. Assuming the latest fixes are implemented, this will probably be as compatible or even more than the two main standalones.