Right, but you don't to wait for your check in time (1PM for the poster I quoted) to board - you just wait till the queue moves which is likely just a few minutes. And once that is done, anyone checking in after that, simply walks on, regardless of what your check in time was.
Most reports indicate the same thing you were told - you can't apply the on-board perk to a pre-cruise purchase. Even combining the two discounts off the on-board price is most of the time a no.
It is unusual for MTD to not be available - if you want that, try to get on a wait list.
You can book any of the specialty venues at any of them as soon as you board - they don't have to be open. They should also be available in the app.