I guess if they make the tools complex enough.... Dreams for the PS4 is basically such a thing.
A more complex creation process would be the only way it would work, and that is not a bad thing. Many people just want to play the levels rather than create them, and it would give options to creators between using a simpler Mario Maker game or the more complex Zelda maker.
Anything other than that and yes, your concerns would come into fruition. However I do not think that anyone who wants this truly wants nor expects a Zelda skin Mario Maker.