First, I fucked up because I was using Mupen64 Plus-Next GLES3, which is intended for lower end hardware and I think is still in WIP. Full disclosure, I didn't own a 64 growing up, so I don't have childhood memories of extensive gameplay on original hardware to compare emulators to, so if you did, you'll probably notice incorrect sound or graphical glitches that I'm likely to miss.
So I downloaded the correct version Mupen64 Plus-Next and tested it with Super Mario 64, Star Fox 64 and some console pushers such as Perfect Dark and Resident Evil. From what I saw, I was able to up scale to 1440x1080 with enhancements and I didn't see any glitches. This core also has support for vulkan.