The solution is using a distro that has support for containers (flatpaks preferably) but doesn't force them on you, so far I haven't found a single use case in which they're truly needed on desktop so apt update still does everything for me.

There's some software that I compile myself (emulators), it cannot be upgraded with a packet manager but that has always been the case.

I use Linux MX but there are other distros with the same approach. It also makes it really easy to see if you're installing them because flatpak is a separated repository from non-container apps (I think it's also updated by the package manager but I haven't tried so far).

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.

I can still do that, because I understood that problem when it arose.

On Mint everything updates automatically for me, Flatpaks and all.

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

you could use topgrade to update, and it will generally update with every package manager available.

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.

Check out Nix, which goes in the opposite direction. There isn't really a distinction between the system and applications.

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.

Well, that's Fedora, my friend. On Gentoo it's still the same.