Some high gain stuff just has some extra nastiness in the high end, but it’s even there on professional recordings that were done with real amps. Go check out some of John Petrucci’s isolated tracks, I was listening to them a couple weeks ago and noticed the exact same frequencies popping out that I generally try to kill with a PEQ.
Pre-Cygnus, I used to put a PEQ after every cab block to tame 3K-4K, that’s always where I’d hear the offending frequencies. It’s tricky to not spread it too far and drop too much out, but there’s some sweet spots. I’ve gotten rid of almost all of them post-Cygnus, but I still keep it on some. There’s also the multi-band compressor that can help tame things without cutting too much out, you get a little more control with the MBC. Leon’s got a video for that, too!
Also to consider, while it might be annoying to play by yourself and hear those, in a mix, they’re sometimes the one thing really making the guitar pop out on it’s own.