Technically, yes, but in practice the difference in hitpoints is relatively negligible. With two D MRPs and one E, you get 88.8% damage reduction and the E rated (presuming highest class) will take maybe one to three extra hits to a module before it is knocked out.
With three D rated you get 93.6% reduction until one of them breaks, and only a minor tradeoff in durability (which, as I mentioned, is negligible enough to not matter to the large majority, seeing as the general recommendation is to fit Ds).
Anyway, yes, it’s beside the point. And I don’t know why Frontier decided not to offer an E rated multi-limpet controller variant, but that’s really only something they could answer. Or address. Maybe they just though offering C or (depending on type) B rated was enough, with an A rated version available for the universal controller (which is not something a new player will be too inclined to pick up anyhow).