You are right about the problem of not being able to control or even see which Mastermind effect you are using at a given time, so being unable to manage when Masterminds finally get discarded from play. The new interface being worked on is using different buttons to denote Mastermind effects coming from different Masterminds (though at the moment fails to show from which actual Mastermind they come, which I hope will be added before release).
For the rules question about the Masterminds staying in play in the scenario you describe, the Menagerie rulebook gives the AFAIK most recent version of the rule about "Throne Room plays Duration" at the bottom of page 2:
Additionally, if a Duration card is played extra times by a card such as Mastermind, that card also stays in play until the Duration card is discarded, to track the fact that the Duration card was played extra times.
So for "Throne Room 1 plays Throne Room 2 plays a Duration card 2 times, then Throne Room 2 plays another card 2 times" scenario, only Throne Room 2 is playing a Duration card "extra times", so Throne Room 1 is discarded this turn.
But Mastermind is both
a Duration card and
a card that can play other cards multiple times (Throne Room is just the latter).
So in your Mastermind scenario (using turn numbers to refer to the Masterminds played), MM10 plays MM11 3 times, so MM10 stays in play as long as M11. In turn 12, MM11 plays 3 cards 3 times each, including MM12, so again, by the above rule, MM11 stays in play as long as MM12. At tend of turn 12, MM12 is not discarded, as it has stuff to do next turn. MM11 is not discarded, as it played MM12 3 times, which we just determined is not discarded this turn. And finally, MM10 is also not discarded this turn, as is played MM11 3 times, and MM11 is not discarded.
That chain of Masterminds will stay in play until one Mastermind finally plays no Durations cards, or Duration cards that at least don't play other duration cards multiple times.
I hope that explanation helped, if anything was unclear, please ask.