I don’t think it really matters much, as long as you’re getting your updates. Personally, I prefer to do my updates from the command line. It just feels faster than waiting for Discover (KDE software store GUI) to load my updates. (I’m a Fedora user too)
Oh, also, Discover does a bad job of reporting errors, in my experience. My Flatpak updates regularly fail, and it was easier to figure out why when I used the command line (my VPN gets blocked, I have to switch to a different server).
May I suggest instead using topgrade? (You’re missing firmware updates, by the way). I haven’t started using topgrade to actually do updates just yet, but I did use it to learn about new kinds of updates I could be making. I just run topgrade --cleanup --dry-run.