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"Take these three items, some WD-40, a vise grip, and a roll of duct tape. Any man worth his salt can fix almost any problem with this stuff alone." - Walt Kowalski
"Only two things are infinite - the universe, and human stupidity. And I'm not sure about the universe." - Albert Einstein
Also, for my money at least, I always try to make the tuner the first thing my guitar plugs into.
If it's in the fx loop, it's going to be seeing the preamp/pedals/gain stages of the entire setup, which would more than likely make tuning less accurate.
But your point about accuracy is a very valid one..
Distortion or EQ has no effect on tuning accuracy, since they don't alter the frequency.
"Take these three items, some WD-40, a vise grip, and a roll of duct tape. Any man worth his salt can fix almost any problem with this stuff alone." - Walt Kowalski
"Only two things are infinite - the universe, and human stupidity. And I'm not sure about the universe." - Albert Einstein
When I was being taught by Guthrie Govan, he always tuned his guitar on the neck pickup with the tone rolled off completely. His argument being that you were effectively increasing the intensity of the fundamental note by dulling the harmonics as much as possible.
Whatever is correct, I'm always most comfortable going direct to the tuner from the guitar for the most accuracy.
With a guitar that has the neck pickup at the 24th-fret node position (which is most, on guitars with 21 or 22 frets), you don't want to use that since it will be more likely to have an odd mix of harmonics.
I've never found distortion pedals to be any problem for a tuner either. Maybe it depends on the tuner.
"Take these three items, some WD-40, a vise grip, and a roll of duct tape. Any man worth his salt can fix almost any problem with this stuff alone." - Walt Kowalski
"Only two things are infinite - the universe, and human stupidity. And I'm not sure about the universe." - Albert Einstein