I could be wrong but the main reason for using wipe on poly on a guitar is to keep the coating as thin as possible so it doesn't interfere with the tone.
Honestly, I think it more about practicality. Most people either don't have proper spray equipment, or lack a work area suitable for spraying (even rattle cans). Also, if they're fortunate enough to have the space for spraying but not have a gun and compressor, rattle cans are notoriously susceptible to orange peel.
Whilst wipe-on takes many many coats to build up a deep clear coat, it's generally an acceptable trade off to having to level out orange peel or runs.

I am in no way saying you can't get a great finish from rattle cans. I seen some that are unbelievably good (not necessarily mine ).

I think that's more important with hollow-body guitars and if I'm honest even then I reckon the "tone wood" debate is way over-stated with electric guitars using pickups that read a magnetic field and amplify it electronically.
I definitely agree. I won't say that wood type has no effect on sustain or some other acoustic properties, but I too think it has been built up as hype more than anything.