I'm very, very new, so take it with a grain of salt, but in real life as in HBD, I'd be more concerned with the aggregate stamina of my rotation than the individual stamina of my 5 SPs. If my top-3 are going to be horses and eat 7+ innings every 5th day, I'd be a lot more willing to roll with a pair of 50-55 stamina guys with good stuff at the back of my rotation (i.e. what most people would call really good LRAs), on the assumption that I can use up a very high % of my bullpen innings on those 2 slots. On the other hand, if my top 3 are great pitchers, but more of the 6-inning variety, I'd be more inclined to live with a little worse stuff out of the 4/5 slots to give me a consistant 6 innings. Additionally, I would try to split my lower-stamina starters apart in the rotation, rather than pitch them on back-to-back days, so that your best relievers are more likely to be fresh on the days where there are likely to be the most bullpen innings available.
I also have a situation where a LRA is my best RP. So I list him as Closer A, with my real closer as Closer B. I then give him a very low TPC (20ish), but a very high MPC (80ish), and set him as available any time after inning 5. He eats a high % of my bp innings this way, and often in high-leverage moments. I could make him my SP #5 but I think I get more productivity out of him this way.