I can't speak for anyone else, but for me, it's just one file to backup to keep all your custom commands (.bashrc) while it would be many files if you have a script for each.
I can't see the benefit of having a script for just one command (with arguments) unless those arguments contain variables.
If you have "keep above other windows" enabled, then it seems to wok as it should.
The context menu is (if I understand it correctly) a window in it self, so it would be behind a window that is kept on top.