You make good points, so I'm not going to delve too much into the whole list. I just wish to clarify two specifics on which we don't seem to see eye-to-eye:
As I understand it, not only has the USN only ever bought strike-length Mk 41, but nobody has bought the self-defense length at all. In any case, I doubt the strike-length are all that much more expensive per dollar, and topweight simply isn't an issue on this hull. Might as well have the opportunity to carry something like N-ATACMS if that ever is deemed necessary.
Dunno about the Mk.41 SD not being used by anyone, both the Aussie ANZAC MEKOs and upgraded Adelaide/OHPs are listed by Jane's with a Mk.41 mod.5 for 8 NSSMs or 32 ESSMs, for instance. In any case, what I had in mind was the
Mk.48 (PDF warning), either on-deck as on the Murasame or City (Canada) classes or grafted on bulkheads as on the modernized Karel Doorman. Both versions minimize the structural impact compared to a Mk.41.
But again, the question mostly makes sense if your design veers towards a more modular approach with stackable VLS blocks. If all your VLS cells are built-in, of course it is necessary to have some strike length in there for mission payload. But if you're ready to resurrect the NTACMS, you're so far away from an off-the-shelf design that you might as well go for a tactical-length Mk.41
I envision a mission bay aft, yes. Probably not a baby well deck or anything, but a stern door that could be served by a LCU or equivalent. I want to avoid mission creep in this sense particularly: this is an amphibious support ship, not a landing platform of any kind.
Granted, there is a risk of mission creep, but also a major plus when seen only from a logistics angle. Keep in mind that a lot of countries with limited ship-to-shore infrastructure use landing craft without the least warlike intent simply to service their more unequipped shores. As soon as ship-to-shore logistics happen (and they will), your costs and transfer rates will be abysmal if you rely only on helicopters.
A dry well deck with a small ramp for RHIBs and Griffon-class hovercrafts, and/or a mobile RO/RO ramp to load LCUs bow-to-stern at low speeds, are both good compromises IMO.
Also re. azipods, I don't know about the USN criteria, but outside of the USN, at least the French Mistral and Spanish Juan Carlos/Canberra LHDs rely on pods while fully militarized.