PRS SE custom 22 - deformed nut groove : continued

Out of curiosity. Why compensating the nut itself is a bad idea? To me (a complete novice) it seems like the easiest solution. Adding wood fillers, shims or veneers, seems much more difficult...

It's not that you can't compensate at the nut, but I think that would be a harder approach to get dialed in correctly. The edge of the fingerboard should be at the right spot and the nut should be at 90 degrees to ensure the strings are at the correct length. I'm sure there are people out there that have compensated the nuts to correct for intonation on acoustic guitars where the bridges are not adjustable, but I've never tried to do it.

Really at the end of the day, it's just about getting the scale right for intonation. What is the easiest way to get that done?