It depends. Kind of prefer Flatpaks as they are always working as expected on any distro, but some of them are giving me just too much struggle.
For example, dealing with sandboxing, or especially VSS code app. Yes, there are instructions, but then I install Golang SDK via Flatpaks the hard way (using CLI) for Go development, then having a nightmare trying to setup everything in vss code. Then how tf should I access go binary within my host terminal?
On Arch Linux I just tend to install from official repos, while the rest of apps - from Flatpaks.
Personally I don’t like the way they are sandboxed, bit as long as it works I am fine.