Afaik "apt install lazarus" installs from the linux distro repository.
That repository is maintained by the makers of the distro (Debian in your case). We (the Lazarus team) have no influence on that.
Our installers can be found on the Sourceforce page, linked on the left menu of this forum.
If you update, Lazarus keeps your config. But your Lazarus executable is replaced by the latest version.
Since installed packages are compiled into that executable, and since we cant know who has which package installed, the new executable does not contain any packages, and therefore must be rebuild once. I am not in charge of the Linux installer, but afaik this rebuild is left to the user.
I have no idea why you need the rebuild in "components". This should be included in the Makefile in the main directory.
You should also be able to go to menu "Tools > Build Lazarus" instead.
Again I am not the expert on Linux. But given that there appear to be wrong ppu files.....
On linux, rebuilding the IDE (as NONE root user) creates a shadow copy in your home folder ~/.lazarus
This is where the ppu should go.
This is where the ppu of your previous builds are.
And this is where your config is.
If you rebuild as root, I do not know if all that is found (since root has its own home dir).