Ok so what do I do when he is actually awake during the night? Leave him to crawl around and wait until he cries for me?
Yep, if he's happy, leave him.
At the moment, we have developmental stuff happening here too and DS lies in bed happily for over an hour after he wakes, chatting with his dummies and creating his own little imaginary world for them. His night sleep in incredibly short (getting down to 8.5hr some nights - this from a kid who used to STTN 13hr at times) but he's fine in himself. Barring pain/discomfort or extreme OT, babies really do self-regulate pretty well provided their world is predictable, hence EASY routine.
But how do I actually know if the afternoon A time is correct if I have to cap it at one hour? I have never waited the whole nap to actually see when he wakes naturally....
If you're capping at an hour, its enough that he's getting to an hour.
Developmental stuff often leads to whining and grumping anyway - wanting to do something, being so close and yet not quite there is really frustrating.