So, I'm not gonna pretend flatpak doesn't use more space then normal apps, but due to deduplication (and sometimes filesystem compression), flatpaks often use less space than people think.

[nix-shell:~/Playables/chronosphere]$ sudo /nix/store/xdrhfj0c64pzn7gf33axlyjnizyq727v-compsize-1.5/bin/compsize -x /var/lib/flatpak/
Processed 49225 files, 21778 regular extents (46533 refs), 22188 inline.
Type       Perc     Disk Usage   Uncompressed Referenced
TOTAL       53%      898M         1.6G         3.6G
none       100%      499M         499M         1.0G
zstd        34%      399M         1.1G         2.6G

[nix-shell:~/Playables/chronosphere]$ du -sh /var/lib/flatpak/
1.7G    /var/lib/flatpak/

I only have one flatpak app installed, and du says that takes up 1.7 GB of space... but actually, when using a tool that takes up BTRFS transparent compression into account, only half of that space is used on my disk.

I recommend using compsize for a BTRFS compression aware version of du and flatpak-dedup-checker for a flatpak filesystem deduplication aware checker of space used.

I think flatpak absolutely does use up more space, because yes, it is another linux distro in your distro. But I think that's a tradeoff people accept in order to have a universal package manager for graphical apps.

Also, you can flatpak cli tools. They are just difficult to run at first because you have to do the flatpak run org.orgname.appname thing, but you can alias that to a short command. Here is a flatpak of micro, a terminal based text editor.

(I prefer nix for cli tools though, and docker/podman/containers for services).