Don't worry about the 'overwrite.' It's still available by using the Uninstall option. "Compressing" doesn't have the 'overwrite' problem, just take a few hundred more MBs.
If you'll notice, the Safari icon, is actually for a 'bundle' folder, also known as an ".app," which you already know is actually just a 'special' folder, a "package." SO, what is 'overwritten' is actually not that icon but the file(s) inside it. And, as I say, the original(s) are still available by running the Installer and selecting the Uninstall option.