Short answer: there is no reason your master password has to be the same
In the mean time, don't get confused by the term "master password." First, you really have to customize your super gen pass with that 'tack on password' (I forget the official term). I would like to see this as the default main page. By putting nothing in the tack on password, you'll get the same password generated as you would now with the simple version un-customized version. You can customize your version by going under the FAQ in the Advanced section. In this way, your super gen pass is different from everyone else's and that rules out anyone doing a dictionary tack using super gen pass. Grab some random characters from
https://www.grc.com/passwords.htm and memorize them and use that to customize (FAQ->Advanced) the bookmarklet before you bookmark it. Your customized bookmarket stores this in clear text so you could fetch them back out if you look in the properties of the bookmark(let).
Finally, there is no reason your master password has to be the same. Just take letters from the domain, user name, and the domain in the username (if present, ex: google apps domains) and use them in your master password. Now your password is different from every site. If you think you'll store super gen pass on a slightly less secure computer (windows), you might want to get a few more random characters and use those in your master password too. Remember, your still at some point you'll have to do this little riddle as software can't account for every web form variation. This may sound like a lot but (after setup) it really is fast and scales very well. It does not take any longer to log in.