While it's not the end of the world, it's just plain annoying having to remove such a common sense feature. The consequence of this means that if you were to distribute a web browser via the MAS, you will not be able to ask the user to set it as the default web browser. That's just a subpar experience.
My hypothesis for the added restriction is that it might be considered a security hole for an app to just set itself as a handler, for say, http links.
The correct way to have handled this particular situation was to introduce a new entitlement and define what content types an app might want to handle, which will get reviewed by the MAS review team. Unfortunately, the solution [2] is: "There is no solution; it can't be done anymore in the sandbox."
[1] http://stackoverflow.com/questions/26241689/lssetdefaultrole...