What is this, and why does it pop up every other day and show a list of updates?
I take it your using Ubuntu, which version? Ubuntu by default checks for updates each day usually close to the time you boot up. It will them present a dialogue of any packages that have update candidates. Most of the time it’s safe to go ahead and allow it to update.
I’m not sure what your reference to Free Desktop is. You might want to take a screen shot and share that so we can see it.
It’s got something to do with Flatpak; I do prefer to know what is being installed before I give it the go-ahead… 
Yes flatpaks are massive creatures and take ages to install, here is a Reddit link to answer as to why they are so big and what it is installing. https://www.reddit.com/r/linuxquestions/comments/98rl37/why_are_flatpak_items_in_software_manager_so_big/
This is generally a problem with models that encourage huge dependencies. I think the most infamous programming language for doing that is probably JavaScript. It’s “normal” to have hundreds of dependencies in a JavaScript project.
If the Flatpak people come from such a background, it does not surprise me that they throw in such a huge dependency into their packages…