I have been wondering for quite some time why some updates can only be updated via discover, never to appear in pamac/GUI, while all “normal” ones do appear, forcing me to use both pamac and occasionally look at discover.
Here is an image of what updates both think are currently available:
I am not 100% certain about this, but I believe it has to do with dependencies. The three actual application updates are listed in Pamac, and all of the other updates from Flatpak are for various dependencies. Pamac installs a Flatpak alongside its dependencies, and should do the same for updates. Due to the way that Flatpaks are containerized, it’s not very useful to show the dependency updates seperately.
As for the UEFI dbx update, Pamac does not support firmware updates while Discover does.
That part is a bug in Pamac. It always underestimates the sizes of Flatpaks because it only looks at the size of the highest level package. Try performing an update in Pamac as shown in your screenshot, and click on the arrow in the bottom right corner of your screen. You should see in the logs that all the other packages listed in Discover were updated.
Well this was weird, i did the upgrade in pamac, and it did the “11MB” update. I then selected from the menu “refresh database” and it started downloading the rest of the updates!? Without ever displaying them or asking me if i want to install them.