The tricky part is that Distro makers, especially ones maintained by companies (I.E. RHEL, Ubuntu, SUSE, and Pop!_OS to name a few) are trying to balance internal company politics and guidelines with external community ones.
Now, I don't know exactly how GNOME theming works from a technical standpoint (outside the fact that it uses CSS stylesheets), but if the "theme" is globally set across all GTK3 apps and can't be configured on a per app basis, then "Other alternatives" for many companies trying to get their distro to stand out probably won't be viable. We've had our own fights internally with building internal tools using colors either not in the style guide or colors reserved for specific uses within the company. Those will, more than likely, trump the dev's desire to not have their apps themed by default on OSes like Pop and Ubuntu as there are usually company mandates to keep the software themed to match the rest of the company marketing materials. And love it or hate it, those style guides make up a huge amount of the look for a company, especially from a customer/consumer perspective. So, until good theme support is added or the ability to not theme all GTK3 apps globally is added, I think this will continue to be an issue.