Yes on the first half of your post: line quality/thickness differential between v5 and v6 on MacOS. Additionally, for me, it was machine specific as well. 5K iMacs were fine (perception) between v5 and v6 with same default Display Modes settings. MacPro with 3rd party 32" 4k set scaled, not fine - very poor line quality default setttings. The fix was to bump up line thickness as you’ve discovered.
Regarding your primary question: I don’t know about separate com.mcneel.rhinoceros.plist files, but if not feasible, what you could do is simply make two Display Modes named Wireframe v5, Wireframe v6, etc., configured appropriately.
In my case, it’s time to commit to v6 in production. Can always go back to v5 if necessary, which I’ll assume will be minimal, if ever…
For reference: