Alright, it wasn't a result of the switch in CPUs.
It was a game client I had on in the background. The moment the client was closed, the skipping resumed immediately. I've gone through several games I have on Steam now, and it seems like when any of them are running, the audio from iTunes stops skipping. It appears some common process that games on the Mac use rectifies this issue.
In the interest of providing a common, free client for people to try, and possibly use as reference for a fix, I looked up open source games for Mac. "The Battle for Wesnoth" (
https://www.wesnoth.org) appears to fix the issue as other games do, and being open source it might be possible for someone to identify the core bit of code that could then be run as its own application? I haven't bothered trying the game beyond launching it and turning off the game's music, so don't take this as an endorsement.