Yeah, both have pros and cons. I have Steam installed through pacman and flatpak also. For me I have the Flatpak version because it contains its own version of glibc. This mostly doesn’t matter, except I play Squad and it’s doing something with it’s anti-cheat that isn’t supported in the most recent versions of glibc, so I use the Flatpak version for Squad only.
Flatpak is essentially a more controlled environment. It will contain everything it needs to work, which is good for ensuring it works but bad because you’ll have duplicates. It mostly doesn’t matter which you use, but occasionally it does.