I use flatpak for virtually everything because sandboxing your applications from each other and from your private data is a great idea to improve your system security. This helps prevent one compromised app from taking actions that affect the rest of your system.
For example, I have the VLC flatpak and used flatseal to revoke internet access because I only use it to play files. If a file tries to exploit VLC, it will not be able to upload any data or communicate with the attacker’s servers. I revoke any permissions my apps don’t actually need.
There are a few exceptions though. I run development and administrative tools directly because I do actually want unrestricted access to the system for these apps.