Sadly I'm pretty sure I'm the only one who cares, but for anyone else who is cool enough to use this application with N64 VC, I found an easy way to fix the analog control. Whatever game you're playing with full 3d analog control, there needs to exist a setting in it's corresponding .ini in the content\config folder.
[Input]
StickLimit = 90
The thing is, this particular settings option only seems to have been added to the emulation somewhat recently, so you'll most likely need to swap out the RPX as well with a newer one that will recognize the config.