don't hate it. It's just an oddity in the soundfont choice for an odd N64 game (arcadey gameplay. there's a training range that is nothing like the actual game save maybe two missions, there's a model viewer on a N64 game [the models themselves are alright, it's just unexpected], you have to beat the game three times to get the good ending, etc)
Looking at the soundfont it's actually pretty far away from Mario 64 save the flute synth, strings, and trumpet.
Knowing how horrendous SM64's soundfont can sound when applied to MIDI it works well with Evangelion's soundtrack.
The only problem I'd have with it is that it would take me out of the experience, but when I played through it the only real offenders were the main theme and the credits, both of which aren't really gameplay-focused. And it isn't really offensive, just funny to picture the horror of EoE and the psychological themes of NGE applied to Super Mario 64.