Anything that puts a dog into a state of fear causes defensiveness. Putting a dog on the defensive is not only mistreatment, but it's dangerous. Scruffing, grabbing the scruff or muzzle as a punishment is a big, huge mistake. Alpha rolling is based on inaccurate wolf studies which have nothing to do with what they know of wolves today and most certainly nothing to do with domestic dogs. All it tells them is that they might be killed, so you can imagine what a state that can put them in. No, what you did...those few times isn't going to impact your dog if you build trust and use good, sound training methods built on trust and motivation.
Rolling a young puppy or an adult over on his back in play or as a gentle, friendly gesture for a belly rub or other play is not the same thing. Don't confuse that. But rolling a dog over as punishment, with anger and forcefullness is a big, huge mistake. So is grabbing near his neck or face in anger. You want to associate grabbing his collar with a good thing in case you ever have to grab his collar for safety. So, gently hold his collar and feed good treats. Do this like an exercise a few times a day. Gradually build so that you exert a little pressure or pulling, associating it with tasty treats and praise. Then work up to grabbing at it hastily, with pressure, feed and praise. This way if you ever have an emergency and have to grab hard at his collar, he won't turn and bite you, which is apt to happen without this conditioning.
As far as the time outs, I agree that since the time out is of some duration, it is hard to pin point a spot in that duration where it will be connected with the "crime." However, I have found that very short periods of isolation for certain behaviors do get associated with the offense. And that's because the dog is removed from what he loves.....socialability. He is isolated immediately and for only a minute or so. Then returned to the group for another try. The act of walking away, (the very first seconds) from the family group begins the isolation or acts as a conditioned negative punisher...(it signifies what's yet to come and the ending of the good thing) and it happens within 1-3 seconds of a given behavior. So, it is not the duration in and of itself which I think is the effective part of the whole exercise, but rather the conditioned response thing which is really working. Sequence: snarky behavior, immediate removal from the group, which becomes a predictor of a minute or so of boring isolation, (bad thing)... return to the group, reinforcement for good behavior. Repeat as needed. Soon, dog connects that there is a condition: snarky behavior, and a response, leaving the family. Good behavior, stays with family and gets treat. There is a contrast for him to experience if repeated enough times so that more reinforcers can be given for good behavior etc.
For example, Lyric was getting snarky with Jose` for a while when they were in the den with me...that was the only time. Lyric seemed to be possessive of me and/or the den. I quickly marched him into another room, right next to the den, was quiet, but swift. In 1 to 1-1/2 minutes, I invited him back into the den, being very careful of Jose` and watching. I started giving treats while he was being "nice" in association with being in the same room with Jose` and me. It happened a few more times and I repeated the isolation....the leaving the room with his snarky behavior. He hasn't acted that way for months. I watch and continue to give treats intermittently while all dogs are lying down, minding their own business when in the den with me.
So, that's my take on the subject. LOL.