Unfortunately, Mac (integer scaling) and web (with the takeover of 1px[*]) have driven this UI concept that everything has to be scaled up for High-DPI screens. And early Gtk+ 2.* versions would gladly take any font size and resize UI elements so the label fit.

[*] though in all honesty, 1px as a relative measure of angular size is fine, it's just very badly named — I was hoping web designers would switch to ems in early days of the web, allowing users to control everything through font size directly — but that would still require some smartness not to increase padding too much with large fonts: basically, we'd want something like flexible spacing a-la TeX's hskip/vskip/hglue/vglue but catering to the screen and nuances screens possess.

Almost no UI (including web pages) is designed to work well with custom font sizes today. It's a definite win of form over function, or at the very least, recognition that designers are unable to design truly fluid/responsive interfaces that they like the look of.

Gnome still allows you to make use of gnome-tweaks to adjust just the font sizes, but you still run into issues because spacing can be too small (thus I tend to run with 125% scaling and 1.4-1.5x font sizes on HighDPI screens).