The questions are in the title, picture is below, but here are the (TL/DR) details.
About 9 months ago, I bought an electric guitar "kit" and assembled it (fun, highly recommended). This included fret leveling, crowning, and polishing. A guitarist friend of mine acted like I might as well go over Einstein's Theory of Relativity and see if I could find some mistakes—it's that difficult! But it went well, in my opinion.
I got the intonation pretty close at the 12th fret through normal saddle adjustment, but ran out of travel on the 2nd and 3rd strings, and had to reverse the individual saddles to get them spot-on. The only problem I still have is the intonation on the first few frets, not so much on strings 4-6, but it's pretty bad on G(3rd), somewhat bad on B(2nd) and merely noticeable on E(1st). They sound sharp, bad on the 1st fret, better as you go up until about the 5th fret is again spot-on. Google tells me that this is pretty common (though I have no explanation as to why G is an especially fickle string!).
I've come to appreciate that if you squeeze the crap out of (example) the G string on second fret that this causes A to become really sharp, and if you just barely touch the fret, it's not so bad, but even when I'm barely touching the fret, which is not gonna happen in normal play, it's still almost 25 cents sharp.
Some of the advice on the internet tells me to flatten the entire string slightly so that the G is slightly flat and the A is only slightly sharp, but, like, I mean, what the hell???? Other advice I've seen is that I'm probably being too critical; nobody else will hear the difference. Trouble is, I don't believe it. Barre chords sound fine, and when I'm playing at or above 5th fret, even perfect. In this case, every string is fretted, and any slight sharpness due to squeezing the string against the fret is equal across the board, probably unnoticeable. But, when playing open chords (especially, for instance, "D", as 1st - 3rd strings all are fretted at 2nd or 3rd fret, yet 4th string is open), it sounds bad. Even open chord "E" has a big problem of the G string fretted at 1st fret (worst string, worst fret, followed by two open strings).
I've been considering trying to shape the individual frets under 3rd string frets 1-3 slightly back (toward the nut), but this seems really scary (worse than the Einstein thing!), especially seeing as how I'm pretty close now.
(cue dramatic orchestra hit)
I was changing the strings on my Ibanez Acoustic I've had for about a year and a half. While cleaning the fretboard, the light caught the frets in such a way that I could see slight dents(?) under the 1st, 2nd and 3rd strings. Heaviest (dark red circles) on the 1st fret and getting lighter on higher frets until they seemed to completely dissapear on the 6th fret (green circles):
The flash obscured the similar dents under the 3rd string, but they're there.
Now the wheels are turning again: Are those indentations there on purpose for intonation? Can I apply this same technique to my electric, relatively* easily? Any other thoughts/methods I could try to help this?
Or is it more likely that I am completely, irreversibly insane?
* thanks, Einstein!