APT is the classic way of doing things, pre-compiled binary packages are installed to your system and they have direct access to your computer, everything works as expected and you don't have any sort of sandboxing or abstraction layers to break your programs, slow them down or introduce issues.
Flatpack and snap are what they've been trying to push for the last 10 years on unsuspecting linux users, they sandbox the everliving shit out of everything.
For most single user home users, this is completely overkill. You're not running untrusted, random installers downloaded from the internet like you would on windows.
Imagine mounting a virtual disk for every program you run, every time it runs.
If you write shell scripts, you'll realize that every single command you write is a separate program and having each of these introduce a delay to spin up a sandbox environment is going to slow you down immensely.
I also have problems with flatpack and especially snaps on principle, they introduce the issue of installing hundreds of versions of the same libraries everywhere on your system instead of one like on APT-based distros, making them extremely bloated.
Last time I checked, snap server software is not FOSS, you don't actually have a choice in refusing updates, they laid down a whole framework where some packages will require up front payment before you can download them, and it is a clear attempt by cannonical to Embrace Extend Extinguish
(https://en.wikipedia.org/wiki/Embrace,_extend,_and_extinguish)
the linux ecosystem.