Nstarz! I read those papers. They make sense about causing fear and so on in the animals and about always having to maintain the "power". I'm just curious if you know if that's always the case. The positioning thing. Because when I used those techniques on my girl is was never about making her afraid. I was always pretty calm. And soothing her. It was more about trying to make her relax and realize she didn't need to be on the offensive. I'm wondering if that isn't recommended either?
I would hesitate to say 'always' because there's always an exception to the rule. Positive punishment works in some cases, in the short term. A punishment needs to be delivered within a short time (2 seconds or less, I believe, but don't quote me on that) for the animal to link the act with the consequences. So your timing with punishment needs to be impeccable (this includes things like alpha rolls and dominance downs). A lot of people can't do that precisely (which is one of the big reasons that rubbing your dog's nose in the soiling hours after the incident doesn't work). So the dog is being punished and it doesn't know why. Which can lead the dog to feel that it needs to protect itself (hence increased aggression seen with these techniques).
You may very well not be projecting a fearful state when you roll her on her back, but that position is very scary for dogs to be in. She probably feels very vulnerable in that position. A big misunderstanding in the dominance-based training world is that a) wolves have a strict hierarchy and b) dogs are competing with us for resources/status in the 'pack.' A wolf pack is made up of a breeding pair and their offspring, So the breeding pair is automatically the most "dominant" in the pack because they are the parents (and those pesky cubs better listen to mom and dad! Lol.) When wolves are of breeding age, they leave the pack and start their own. Furthermore, if wolves were to show submissiveness to another wolf, it would be voluntary. THe way we do it, it's forced on the part of the dog to be "submissive" when it really creates fear. Also, dogs aren't dumb. They know we're not dogs. They know we control the resources. I think if any species wanted to "dominate" us in the dog-training world sense, it would be cats

I think dominance is about bullying our dogs. I believe more in a mutual, respectful relationship with my pooch, which is why when I ask him to do something and he listens, I reward him with yummy things for making the right decision. Punishment also doesn't tell the dog what TO do, only what NOT to do.
Hypothetically, if your dog were practicing poor behavior, and I wanted to discourage it, I would desensitize and countercondition to the stimulus. So, if a dog were lunging/growling at passing dogs on the street, you start from a safe (no reaction) distance, get a good "watch me" command and then move closer and closer to the dog. As you decrease the distance, ask for a watch me, then reward. The dog will eventually learn that dogs on the street mean yummy things are coming. I would much rather my dog have that reaction to something it used to fear than one it may get from being pinned on its back when it sees a dog (which only reinforces the fear it had already).
Does all that make sense? Sorry, I was rambling. ANd I don't really know if I answered your questions.