I can still do that, because I understood that problem when it arose.
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I actually like Flatpaks... I use dpkg/apt-get for system packages that cannot be installed in userspace, and flatpaks for desktop apps / games. Many distro's have unified ways to update them anyway (at least VanillaOS has)
Your mileage may vary, but it's still possible to install some distros without those nonsensical containerised "package managers", or to at least remove them after installation. It unfortunately takes an increasing amount of effort, especially in distros that are actively trying to push their flavour of containerised package manager. (Totally not looking at Ubuntu and Snap)
What is working in our favour here is the fragmentation, which will prevent, or at least slow down a too widespread adoption of those systems.
Check out Nix, which goes in the opposite direction. There isn't really a distinction between the system and applications.
you could use topgrade to update, and it will generally update with every package manager available.
On Arch Linux I've migrated away from Flatpaks, so I only use AUR and official repos.
Oh boy my updates speed increased like 3 to 5 times. Flatpak is slow as fuck.
Also my ISP is slow as fuck.
On Mint everything updates automatically for me, Flatpaks and all.
This is why I really like KDE Plasma's discover. It's got integrations with apt, snap, Flatpack, and rpm, and that's only the ones I've tried so far.
I don't really use discover itself to manage my packages, cause for some reason I prefer to do it with the cli tools, but it is a great update notifier.
Except it doesn't always work. I've seen it stuck and loading updates forever a few times, while a simple flatpak update command did the job with zero issues.
This is one of the reasons i don't use flatpaks, snaps etc. I get everything either from the official repos or from the aur. Except balena etcher as it is the only thing i was unable to install via my aur helper and i couldn't be bothered to look into why as balena is not that important to me.
It is the ONLY package that isn't updated with my update command as i installed it via appimage