Guitar Setup and how setup affects Axe-Fx

FWIW, the term "guitar set-up" in the context of the instrument is generally accepted to mean "how the guitar plays" as in neck relief and string height typically measured at the 12th fret. A "guitar set-up" involves adjusting the truss, adjusting the bridge height and insuring the string height at the first fret is "correct". Once all these factors are checked and adjusted as needed the instrument is intonated and considered "set up". A "set-up" also includes replacing the strings for optimal intonation.

This is the kind of work lots of people don't want to or cannot do. Adjusting pickup height is rarely ever part of a "set-up" unless the pickup height causes problems with overall tone (e.g - pickups are too close to strings and their magnetic pull actually affects the strings vibrations and makes them warble)

I processed thousands of guitar set-ups during my time in music retail so this is all based upon that experience as well as playing guitar for a long time.
 
just helps you to get an ideal signal to noise ratio
That too, but it also affects how much drive you have in your distorted preamp model, similarly to how a volume knob on your guitar does, but without the corresponding change in tone.

Normally you don't get to adjust the gain until you're a couple of gain stages into the preamp. With Axe you sort of get a transparent boost (or attenuation, if you prefer that) before the preamp.
 
That too, but it also affects how much drive you have in your distorted preamp model, similarly to how a volume knob on your guitar does, but without the corresponding change in tone.

Normally you don't get to adjust the gain until you're a couple of gain stages into the preamp. With Axe you sort of get a transparent boost (or attenuation, if you prefer that) before the preamp.
If you're talking about the global Instrument Level Control, that has NO affect on tone. That is for optimizing signal to noise for A/D converters.

There is no control called "input level".

Are you talking about Input Trim?
 
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