My dogs are pretty similar to yours. One if definitely dominate. The other not so much. Sometimes my dominate one will try to force her weight around in front of me but I always correct her. Why? Because I'm in charge, not her. Our dogs also look to us to take charge and when we don't that's when more serious issues start happening. On the same note, the dogs (both) start losing trust that we can handle the situation.
I think the difference's between how you handle it & I do are the following:
-Catching the aggressor before it touches the other dog (although mine has not seriously hurt him). I know my girl (aggressor) starts by stiffening and staring intensely at the boy. She has her tell signs that I try to tune in to.
-Making them submit to your authority with 1, single, verbal correction; while you physically move in towards the aggressor until they willingly (& physically) back off, turn their head away from other dog and lose focus of the other. That to me is submitting.
I feel when you physically manipulate a dog to move by pulling them away or alpha rolling they aren't really submitting to you but instead are forced to. When they willingly back off from your pressure then you are gaining real ground.
If on the other hand they are in full battle then it's a different approach and you just separate them as best as possible. That's why it's more important to look for the cue's and snap them out of it before it escalates. At this point there's nothing for them to learn from. So,
imo the muzzling or time outs dont mean much.
I also agree that the dogs are confused. I think you need to reel in the reigns and re-establish the ground work with them both again. I know for myself, as the dogs get older, I tend to slack on making them work for things. Then some unwanted behavior will start emerging which I take as a reality check to reel them back in & tidy ship, so to speak. It's just a refresher to keep them in check. If you don't make them work for their food, treats, playtime, pets, walks, work it back in. I understand they are good dogs but reinforcing your status in their world can only help. Dogs really do appreciate structure, which I'm sure you know, but like I said, we tend to slip up once in awhile. And dogs notice everything!
Hopefully my idea's are food for thought. BTW my female has had issues with food aggression since she was a little pup, so unless I am there w/100% attention on them I will only feed them separately. Otherwise, I will correct, redirect, correct, redirect. I do feel something is working as I feel like now she is more "food stingy" then food aggressive..LOL still getting there!
PROUD AKITA MOMMY 
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