I honestly don’t really see it, I think vanilla GNOME looks amazing, while KDE Plasma just screams Windows 7 to me.
Having said it that, both are great DE’s with vastly different approaches. So these can definitely just co exist, while we can both agree that both DE’s are great for different people and workflows.
Flatpaks definitely do follow the system theme by default. I’m running Silverblue, so all my apps are Flatpaks.