As an Ubuntu theme developer, you’re highly familiar with which apps Ubuntu ships by default, and which apps are developed on gnome․org. Maybe that knowledge gives you a mental model of which apps are “system/base apps”. But given that you thought Rhythmbox should have a squircle icon, but Sam now does not, it is not “pretty clear” even amongst theme developers.
As for being “a brand”, that isn’t necessarily a separate thing. For example, App Store, Launchpad, Siri, and Time Machine are a few examples of apps that are integrated into macOS and also have their own brands. In Ubuntu it’s happened once before, too: landscape-client
used to be integrated into System Settings, while also representing the Landscape brand.
Least importantly, it’s not the case that in Windows 10, “system apps have that symbolic microsoft-goes-flat icons. The rest doesn’t.” Here are twelve counterexamples from Microsoft itself:
A typical Windows 10 installation has the same kind of jumble we’ll have: even though some Windows ISVs have adapted their icons to the flat style (e.g. Instagram, Slack, WinZip), most have not. It looks less bad in Windows because the tiles strongly impose a shape of their own.
Agreed, that would be an improvement. I’d put the non-Suru group first, just so that Firefox could go first, to maximize familiarity for new users.