Have you tried just dividing your limit by 7? So, using 7 concurrent transitions where you want no more than 50?
I would agree this sounds like a bug, but maybe you can still get what you want out of Skyline by setting the limit in terms of primary transitions, knowing that they will always come with the extra optimization transitions, over exactly the same retention time range.
Thanks for reporting the issue to the Skyline support board. Let us know if this gets you unstuck.
--Brendan