I want to be able to update only my apps (like Chrome or VLC) using Discover but for some reason even if I use the “Select none” button, the System Software → System Upgrade is still forcefully enabled and I cannot uncheck it.
System upgrade is by definition an upgrade of everything on the system – apps as well as OS.
If you only want to upgrade specific items then use the command line with dnf to select exactly what should be upgraded.
It really is discouraged to do that since linked dependencies also get upgraded and keeping everything up to date and in sync ensures the software always matches – across the board.
When picking and choosing what to upgrade the system can have varying degrees of mismatch with the software in the repos. When you do a release version upgrade it must all be upgraded to the version in the repo before the full release version upgrade is attempted anyway (to avoid potential problems).