...or they dial in the tone based on JUST the guitar tone by itself...which then falls apart in the mix.
Very true. A tone that sounds awesome by itself may be wrong in the mix, or vice versa. You need to be clear about your goals. What are you trying to create? Tones, or tunes? Guitar tone is something guitarists tend to obsess over, too much in my opinion, often to the annoyance of other musicians involved in the project. How many guitar players have we known who insisted on playing too loud, to the detriment of the music because--you know, "gotta get my toooan, dude."
I think you're right about VST presets, presets on modeling amps, and the like. For some reason, the creators seem to like to ratchet up the effects on presets, maybe because it sounds far-out and cool in the music store. Often sounds like garbage in a real mix.