Linux
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Linux is a family of open source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991 by Linus Torvalds. Linux is typically packaged in a Linux distribution (or distro for short).
Distributions include the Linux kernel and supporting system software and libraries, many of which are provided by the GNU Project. Many Linux distributions use the word "Linux" in their name, but the Free Software Foundation uses the name GNU/Linux to emphasize the importance of GNU software, causing some controversy.
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Snap forces updates, and you cannot disable them. So if you use snaps, I guess you can stop worrying and keep going with your usual apt routine.
Perhaps a small bash script to iterate through all of the package delivery mechanisms' for updating everything?
I use Fedora for work, but ArchLinux at home. If you really want to skip flatpak then you need the AUR.
I get 99% of my packages via nix and the other 1% through appimages which I can put anywhere I like on my disk
I think a script with apt/pacman/dnf etc., flatpak update can do the job as well?
IMO its against the unix vision to extend apt to manage flatpak as well.
Which is kinda one of the main reasons I started to like and still like gentoo. I do understand that it's not for everyone as a daily driver. Maybe Arch could also fit?
Is it possible to bring back that experience? A unified, reliable CLI solution to make sure EVERYTHING is up to date?
Yes. Use a Linux distro that doesn't use flatpacks and you're good to go.