the main drawbacks I see are related to the sandboxing of apps, e.g. that several firefox addons that I just, such as the KeePassXC connector don’t work in flatpak packaged firefox, because they require native messaging support which is unavailable in flatpak. There is a three year old bug report on this at github, and an even older bug report in the Firefox bugzilla. Unfortunately, there seems to be no capacity to solve this or this is not a priority, although this problem affects quite a few users. I have similar issues with the Flatpak packages Nextcloud client: Do to the poor system integration, neither autostart works not integration with Nautilus or other file managers, unless you do some manual tinkering (which isn’t particularly difficult, but with native packages it will just work™ out of the box.) These issues have been known for many years, yet there seems to be no activity to solve them.

How does flathub count users, given that accounts are not required?

Actually, you add the nextcloud account either in Kaddressbook or in Korganizer/Kalender, or in Akonadi konsole. There was something called “online accounts” in Plasma but I never understood what it was good for, mostly obsolete instant messaging services, but not the integration of Nextcloud. KDE/Plasma has nowhere near the consistency that GNOME has. Sure, it generally offers more functions and options, but it is certainly more messy.