1. If you want only the fourth line on the phone to display message waiting notifications, set its MWI Policy to Light and Prompt, and set the MWI Policy on all the other lines on that phone to None. You don't need to reboot the CallManager or anything, but you'll want to reset the phone.
2. The X is simply shorthand for "the extension of this mailbox". That's how MWIs are lit by default on the subscriber's own phone. You can have up to ten extensions on that list including the X. And yes, you can remove that X if you really don't want to activate the MWI on the subscriber's extension. Sometimes that's applicable for system mailboxes where the mailbox's extension isn't a phone.