There's a very good point here about the limits of using usage telemetry -- given a question of the form "should we invest in improving feature X?", it's a mistake to decide not to simply on the basis of low usage. Low usage could be because users simply aren't interested in the feature (in which case it probably doesn't make sense to invest in improving it), or it could be that they really are interested in it but they don't use it because of limitations (in which case it may well make sense to invest in improving it).
However, I don't believe that's an issue for the specific features discussed here (userChrome.css and userContent.css). These are by their nature features that are only accessible to users with particular knowledge/skills and the Firefox user base is much broader than web developers. But moreover, nobody is proposing to remove this capability and I think its debatable whether it is now harder to access in practice (existing profiles that use this capability were automatically converted, for new profiles you already have to manually add a file to the profile directory, flipping a preference in addition is not a serious barrier).
> I don't know if it's a purposeful process or not, but I'd say it's perfectly reasonable for users to think that pref-gating is the first step toward removal
It might be reasonable if no other reason was given, but there is a specific and compelling reason (avoiding unneeded main thread I/O during startup for something like 99% of users) here.