At heart are some opinionated changes by the libadwaita team to disable global styling, which align with an anti-theming petition that some of the team members support (stopthemingmy.app). These decisions wouldn't normally be particularly noteworthy, except that libadwaita seems posed to make its way into "core" GNOME software and would thusly affect System76 and their own efforts in customizing Pop_OS!.
Some of the S76 staff responses are brash, but not without merit. I'm left with the impression that distros are not considered a "customer" by these GNOME contributors, so much as the app developers in their immediate circles that shoulder the brunt of support issues caused by the problems they hope to solve.