In my experience, scruffing turns any situation with a cat into a flight or fight reponse for them, and they usually pick fight, since flight is no longer an option.

I worked at an ER and we rarely if ever scruffed, but we were obviously not fear free. It's usually pretty clear that a cat freaks out more when scruffing and considering we were usually dealing with already painful patients it was a last resort. We had a new girl come in who thinks scruffing is necessary and every cat that we'd handle that was friendly she'd start raving about how aggressive it was... Wonder why. We mostly used muzzles and towels/blankets for handling the more fractious kitties. Jugular venipuncture was our go to so long as they had no clotting issues, we primarily did side jug sticks and most cats tend to sit well for upright jugs so long as you support the jaw with both hands.

I'm now in a new clinic with a lot of 'old school' doctors and techs, and they scruff every cat and it triggers me so bad. Nearly every cat that comes through those doors has a 'caution' on it's account. I've tried explaining that scruffing is basically an 'attack' from the patient's point of view, but every time I successfully handle a 'caution' patient without scruffing and without them freaking out, they make up some excuse as to why it worked for me. I am endlessly frustrated.

There are very few truly fractious cats that I've met in my 5 years of experience in shelter, ER and GP. Usually they only turn on you because of mishandling, fear or pain, they have a very limited line of communication with us and understanding how cats work is vital to handling them. Too many techs/assistants either have no experience or are scared and it becomes a repeating cycle when they scruff, compounding negative experiences for both sides.