Flatpak has its benefits, but there are tradeoffs as well. I think it makes a lot of sense for proprietary software.
For everything else I do prefer native packages since they have fewer issues with interop. The space efficiency isn't even that important to me; even if space issues should arise, those are relatively easy to work around. But if your password manager can't talk to your browser because the security model has no solution for safe arbitrary IPC, you're SOL.
Garuda for me. The reasons are similar; just replace some optimization with some convenience. It's a bit garish by default but pleasant to use.