Well I hate to disagree with all the doomers here, but I don't think flatpaks are the devil. Flatpaks are as good as the person shipping them, there are not many flatpaks that actually have official dev support so a lot of these programs are packaged by volunteers in their spare time. So no, they may not have the best default settings.

That said, I run flatpaks almost exclusively on Kinoite I've never had an issue with flatpak theming or my cursor changing. Some applications are very obviously made for GNOME or KDE explicitly but flatpak doesn't have anything to do with that. Of course if you are running a WM rice or something with very specific theming then that's another story. You can customize a Linux desktop in countless ways, you can't really expect these applications to keep up with that by default (flatpak or not). It's the same concept as something like Discord or Steam, it will look the same for everybody but you can theme it if you put some effort in.

IDEs are another issue, the whole concept of an IDE is antithetical to a sandbox in the first place so it's simply not a very good use case of flatpak. Flatpak isn't a one-size-fits-all solution, that's why even the Fedora immutable desktops give you additional options like rpm-ostree, podman, buildah and toolbox.