I’m likely missing something obvious, but these font inconsistencies are making me rather curious.
I had a look at GNOME Tweaks and Refine, and they seem to be handling font sizes rather differently.
In both instances the Labels appear to be the same size, but the descriptions for the labels differ quite dramatically; so much so that the description text is the same size as the label in Refine; in Tweaks they differ enough to make the UI usable:
I didn’t think I had it set, so I did a find from my Home directory.
I eventually (I have a rather large Home directory) found it in ~/.local/share/flatpak/overrides/global, and, once I removed the entry in there, it all looked correct again.
Amusingly, it never appeared under the “Environment” section in Flatseal, which is why I had missed it initially.
Thanks for the hint, this would have bugged me endlessly.