haven't had chance to read all of this, and only have the one ds, who is 2.9....but, have always let him help himself to food (much to my mothers disgust ). We have an under the counter fridge and ever since he could open it he has periodically considered it an activity to open it, help himself to something, and then munch. (Never shuts that blardy thing of course!) Have regularly come in from pegging out washing or picking up the post from the hall and found him munching on a block of cheese, 1/2 a cabbage, a mushroom etc, etc. I just cut a small amount off whatever it was and put the rest back, never made a big deal out of the fact that he helped himself.
He is now tall enough to reach goodies in the pantry too. Obviously there are times now when I will say 'no you can't have a chocolate biscuit, coz i'm just doing your dinner' etc, but will then distract him by getting him to help with dinner. I think because I had an eating disorder from the age of 12 (mother constantly on diets and very controlling of what we ate, and no I'm not implying this about you honey), I felt very strongly that I never wanted ds to feel that eating was in any way forbidden, and I wanted him to learn from an early age to regulate his own appetite.
I feel to a degree this has been sucessful for us as he will regularly leave the end of a chocolate bar, or half a choc biscuit, or a handful of choc raisins or other food considered 'treats' by others, coz he's had enough, and has the confidence to know that the doesn't have to stuff it all down, coz he knows that he can always have it another time. (that was an abiding memory for me, making myself nauseous finishing a bag of chips that was too much for me, but knowing it could be months or much longer before i had them again, so couldn't possibly leave them!)
Also, given a plate with a selection of food, he will leave bits of all of it (i.e. crisps, sandwich, cheese stix etc) not just eat all the stodge and leave the cucumber, grapes, apple etc. Which tells me he eats because he enjoys the taste and knows to stop when he's had enough. Or maybe I'm reading too much into it. I honestly wouldn't worry too much about it, and if I were you I reckon I would put a snack in his bedroom for him to have when he wakes up (might need to put it out after he's asleep of course). Try and chill out if you can, in the scheme of things it really isn't a biggie, and if you can give him permission to eat it might take the thrill out of sneaking down and doing it. Sorry if i've rambled! hope it helps. hang in there, this motherin' lark can be very hard on us!