I set up all my own basses, most of them have recut nuts. I like a low action. But when the action in the shop is around 6mm at the 12th fret you can't make any sort of connection.
FWIW I tried out a brand new Aerodyne (MIJ) with an eye to purchase, but the setup was horrible and I couldn't bond with it.
OTOH my Squier 40th P (MIC) was set up to (near) perfection.
Shouldn't be an issue with uneven spacing as the end holes ought to be ok and its probably just careless setup.
I agree that overall bridge alignment out by more than one or two threads is likely problematic.
I enjoy the physicality of playing with my fingers, particularly the way I can use fingers an thumb to mute and make different effects I vould never do with a pick.
Pick suits some styles and songs though.