libvte is a major offender here. It's used in several popular terminal emulators, and it's deliberately capped at approximately 40fps[0], which means on a 60Hz display you'll sometimes get an additional frame of latency, and not even predictably because the timing is so uneven.

Set your keyboard autorepeat to 60Hz, hold down a key in a libvte-based terminal, and watch how bad it is. Now try again with xterm and see what it's supposed to be like. I can only assume the slow update is some misguided attempt at power saving.

[0] https://github.com/GNOME/vte/blob/master/src/vte.cc#L10547