Google's recommendation aside, many think you should sign every app with its own key. In a very real sense, ownership (i.e. knowledge) of an app's key is in essence ownership of that app and any other app with that key. There's no mechanism to ever change an app's key.
Another potential problem with signing unrelated apps with the same key is if/when your company grows. It would be prudent to minimize the damage that a single disgruntled employee/partner could do to your business. A paranoid person might even retain sole responsibility for signing apps with the production keys.
If I understand the premise of your second question correctly, then you are correct. Keystores are just collections of keys and the aliases are just a short-hand way to identify each key. You can make a copy of the keystore file and selectively delete some of the aliases (keys).
Use this command to see the commands that can be used with the keytool
command:
keytool -help
Use the following one to see the options that can be used with the delete command. It goes without saying to make a backup before modifying the keystore:
keytool -help -delete