I think something we forget here is that with such a large inventory of rooms, and dwindling staff (as someone else pointed out), that Disney has probably moved to a largely scientific way they approach this topic.
Historical data likely provides Disney with a plethora of information as it relates to check-ins/check-outs (weekday average times, weekend average times, holiday average times, peak/non-peak, etc, etc). This data is likely aggregated to give them the most likely time someone will check-in and check-out. They likely use this, as well as expected arrival times from Magical Express/Advance Check-in, against the capabilities of the Mousekeeping staff to plan their day and help them meet the check-in time they state.
I looked through the lodging laws in Florida but cannot find anything that holds them accountable (by law) to the check-in time. That said, they advertise it as the time the room will be available and need to stand by that declaration. Poop happens from time to time, so I'm sure there's a situation where a room won't be available on a time they estimate (flights early, wrong information they received, slow mousekeeping, etc, etc). Depending on when they think it will be available, they should make reparations accordingly. I think that they do their best to meet their obligation, but like anyone, are prone to errors from time to time.
To the OP, if she's still around 49 pages later, I hope that you are including some thanks for the response you got from the All Star staff. I agree with others that their nighttime support needs to be suped up a little bit, but I agree with others in that their response seems to be more than adequate unless you had your hearts set on the All Star. We, as a culture, need to be better at pointing out the positive rather than harping too much on the negative. As cliche as it is, the power of positive thinking can make many negative situations more easy to swallow.