Hi Nikoloas. I am the author of that article. On Silverblue systems this is expected, and nothing to worry about. See:
NOTE: You may receive several warnings that say something like “Cannot compress permission denied.”. This is because some files, on Silverblue systems especially, the user cannot easily modify. This is a tiny subset of files. They will most likely compress on their own, in time, as the system upgrades.
However, if you are distressed, look in the output. Most likely *all the failures are some sort of permission denied error. I hope this helps!
Unfortunately I didn’t redirect the output of the command to another file, and the terminal didn’t keep the lines output from all the millions of files processed. But since there is a most likely cause and explanation I ll take your word for it.
While googling about it I also decided to run a scrub to see what would happen:
$ sudo btrfs scrub start /
$ sudo btrfs scrub status /
Scrub started: Thu Apr 29 19:11:54 2021
Total to scrub: 333.60GiB
Error summary: no errors found
Your suggestion looks a bit complicated to me because of my setup and my limited understanding of these parts of the system. When Installing Silverblue 33 on my laptop I 've merged two SSD’s into one volume (partition? - not sure what the right term is) and used LUKS encryption on that combined volume. To illustrate: