Assuming both machines are running work that is the same priority. I feel it is more productive to keep the long runtime going non-stop and fill in with the short runtime.
It is hard to get much done in a 10 minute cycle.
Maybe you should give some thought to a manual load pallet for the short run parts, that way machine load time will be less than a minute instead of three.
No matterwhatyou do ther will be times when both machines are waiting for setup at some point in time.