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I can't see an app on a phone being accurate enough. But I stand to be corrected.
Not sure what guitar you have - Some guitars like a Strat and you might need to lower the pick-ups, as pole pieces tend to have an impact on the 12th fret note, from magnet pull
I've never used a mobile app so can't comment, but any good tuner should be fine - I can get pretty close with my ear most of the time
I often then check the fretted note at the 19th fret as well - if it is there or nearly there at the 19th fret regarding intonation, then almost certainly in at the 12th
Other factors can have an input into the actual set-up and intonation - sensible relief, sensible action and a well cut nut plus as I mentioned the pick-ups can cause issues regarding intonation
2. It shouldn't make any difference - the harmonic should always be perfectly in tune with the open note - but pickup magnets (especially on a Strat) can do odd things if they're adjusted too close to the string.
3. It shouldn't, unless the whole bridge is moving.
4. A phone app is easily accurate enough. You can make more difference just by changing your fretting pressure.
I use the TC Polytune app on my phone just via the phone mic. (Although I also check by ear using harmonics vs. fretted notes at other positions than the 12th.)
"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
I try to get no difference between 12 fret and open but don't worry if it's within a couple of cents as the human ear can't detect that little difference
Does the guitar that you are adjusting have a vibrato bridge?
I think I am there now its definitely much better than it was so fingers crossed.
Welcome to the forum!
You may not need a tuner for checking intonation - your ear should be just as good if not better for detecting whether the fretted is flatter or sharper than the harmonic.
Supportact said: [my style is] probably more an accumulation of limitations and bad habits than a 'style'.
I recently bought a strobe tuner and am really liking having the intonation spot on and then using a sweetened tuning like James Taylor's. Seems to sound more in tune but with the warm weather it does not last.