In that case you should use user-install flatpaks and separating and reusing your /home partition

Offline/internal network installs can be handled with flatpak create-usb - https://docs.flatpak.org/en/latest/usb-drives.html

One can distribute flatpaks along with their dependencies on USB drives (or network shares, etc.) which is especially helpful in situations where Internet access is limited or non-existent.

Cache/mirroring would be great for those who need it.

Edit:

Thinking about it, I wonder if there's enough "core features" with 'create-usb' that its just matter of scripting something together to intercept requests, auto-create-usb what's being requested and then serve the package locally? If a whole mirror is required, it may be possible to iterate over all flathub packages and 'create-usb' the entire repo to have a local cache/mirror? Just thinking "out loud".

Flatpak "containerizes" the program, which makes it more secure and less able to accidentally mess up other programs. Fuck if I know how it works.

Also you don't have to type in your password every time you want to update the program, so that's nice.

Honestly, you don't have to worry about what others say, you should use what works best for you. Personally I find them to be nice and comfortable to use, myself 😅