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.

I use BAUH as a GUI "update everything in one click" does repos, aur, flatpak, snaps, appimages. Paru is CLI option for repo, aur and flatpak. I dunno if it does snaps never checked.

100% agree with you OP.

Fedora updates flatpaks automatically, system updates too, but you need to reboot. Which Fedora version do you use?

I use very minimal software and usually don't care about Flatpak

No need to overcomplicate things, just write a small shell script or even just an alias. I use this daily:

alias get-rekt="sudo apt update && sudo apt upgrade -y && sudo apt autoremove -y && flatpak update -y && flatpak remove --unused --delete-data -y"

adjust accordingly for Fedora and/or snaps. Obviously doesn't work for appimages or manually compiled stuff which should be a last resort if there's no other sensible way to install stuff.

edit: voyager shat the bed with the code block but you get the point

emerge -uDN @world

...and head to bed for me.

I use one command to upgrade the whole system: paru one one system and yay on the other laptop.

I'm using MX Linux and don't use any flatpak or snaps, only good old debs

I know that a lot of people share the same thoughts with you but I respectfully disagree. If you want your system to be updated only with your apt/yum/dnf program, then just don't install anything useing snap/flatpak/etc. Sure, you will not have all the apps available in the repos, which was also the case in the past before these systems. Back then, your only option was to compile from source, which was more work-intensive than flatpaks/appimages/snaps. And updating was also much more complicated. Therefore, unless you wanted something really special, you'd stick to your repos. Flatpaks allow developers to distribute their software (and users to install it) in a less labour-intensive manner for the developer. Compiling and testing your app for Debian, Fedora, Arch, SuSE, MX-Linux, Linux Mint, Linux Mint DE, Gentoo, and all the other popular distros is an impossible task for small developers. Flatpaks was a godsend for them and for the users who don't want to compile from source. Now, you can argue that we shouldn't have all these systems (flatpak, snap, appimage, docker, etc...) but one would be OK. And again I will disagree. One of the most important aspects of FOSS is diversity. Embrace it even with its drawbacks. It would require a much longer post to explain this and others have done it already better than I would.

I get 99% of my packages via nix and the other 1% through appimages which I can put anywhere I like on my disk

If you want a single command, consider topgrade. Not sure if it supports Flatpak and Snaps yet, as I do not use those (yet).

I mostly stick to things in the repos, if theres something I want that's not yet packaged I package it myself because Gentoo packages are fancy bash scripts with libraries (eclasses) to handle the normal make && make install sort of things for most build systems

Perhaps a small bash script to iterate through all of the package delivery mechanisms' for updating everything?