1) Yes, a universal app has everything for both versions so it is bigger. For a user that wants the app on both types of devices this isn't really a problem.
2) No, there is no way to have two separate apps such that the user can have both while only paying for one. At least it's not possible through standard means. If you make both apps free with IAP, then you could have your apps generate some sort of code that could be entered into the other to grant full functionality. Such a scheme is a lot of extra work.
Try to do a universal app and see how big it gets. All of the code is shared and as long as you don't have too many iPad-only full screen images or iPhone-only full screen images, the universal app isn't much bigger than a non-universal app.