That's fret wear. The strings have slowly eroded away some of the fret material, leaving those dents. Over a long enough time, they become deep enough to cause problems.
When the fret wear is bad enough, you can have your frets "leveled", which means sanding down the tops of the frets so that the dents are sanded out. Then the frets a re-crowned and dressed and polished and they will be good for a while. Eventually frets wear enough that they have to be replaced, which is called a "refret".
All guitars have compromises on intonation - it's a consequence of the construction and mechanics of the guitar. One thing you can investigate is a compensating nut, which is a nut which has tiny extensions so that the nut side of the strings has intonation adjustments made kind of like the saddle side of an adjustable saddle bridge.
Another factor in the intonation of guitars is the ideal placement of the frets, adjustment of the saddles, and the overall action.
Personally, I do like your friend suggested and I deliberately tune the open strings of my guitars slightly off from where the tuner would have me tune them in order to make a tradeoff for better intonation around the 7th - 9th frets, where I like to play the most. I don't do this on my acoustic guitars, but I do it on my electrics.
Another thing I agree with is that mainly listeners don't notice the intonation quirks of guitars, but in some ways they do but it doesn't matter because that's a part of how guitars sound. It's one of the little details that synths and sample libraries don't quite get right when they try to imitate guitars.