For personal use, Flatpak when there’s no native option, in most cases. They always seem to work and with Flatseal, you can more finely control permissions and local filesystem access of them.
For servers, if it’s a single-purpose VM (like I do with my PiHole/AdGuard servers), I’ll also go native. Otherwise, Docker for compatibility and ease of management.
For personal use, Flatpak when there’s no native option, in most cases. They always seem to work and with Flatseal, you can more finely control permissions and local filesystem access of them.
For servers, if it’s a single-purpose VM (like I do with my PiHole/AdGuard servers), I’ll also go native. Otherwise, Docker for compatibility and ease of management.