You can save a lot of space by deduplicating the files if you use a file system that supports that (zfs, btrfs, ntfs if you can find a driver the supports it).
I use xfs since it is the only one that I have zero issues with. Also, I don't need flatpaks (rarely do), the AUR basically has everything I personally need.
Flatpak already does deduplicating for you on all filesystems.
I've run into a few programs that rarely got updated on the AUR but got regular Flatpak updates. The AUR wrappers are only so good as the people maintaining them...