I don't know if it's just me, but running a command looks like this:
$ gnome-shell-extension-installer 3518
[3518] Obtaining extension info
[Transparent Shell] Downloading extension
[Transparent Shell] Extracting extension
Extension “transparent-shell@siroj42.github.io” does not exist
The last line comes from gnome-extensions enable transparent-shell@siroj42.github.io. I noticed that the shell needs to be restarted before running the command. That means the extension disabled until the shell is restarted and this command is run manually.
Maybe it is possible to add the extension to settings get org.gnome.shell enabled-extensions instead of the gnome-extensions command ?