Well, that and it costs quanta to power those abilities. If the stacked permanents' abilities are used all at once, each consuming the proper amount of quanta, players lose their ability to control their quanta use. Also, specifically with Mindgate, if I draw a Miracle, for instance, from the opponent's deck, I'm probably not going to want more than one of those. Having separated permanents allow the most control for the user as of now. There is no card in EtG which allows its ability to be used for a set amount of times other than one or limited to quanta amount, such as Photosynthesis.