Of course, there is a huge difference. I'd never condone holding an 8 kg cat in the air by the scruff of the neck : always keep his back paws on ground, and as far as the answer linked in the question is concerned, release him as soon as he has swallowed his pill. And don't use scruffing when not necessary.
That being said, having tried to pill my cat without scruffing him, I feel it's much more comfortable for a cat to be scruffed during a few seconds than to be gently tortured during 5 minutes or more. That's a fact. ;)
Now, no other facts, but experts advices (the bold weighting is from me) :
Traditionally, scruffing (grasping the cat by the scruff of the neck) has been considered an acceptable way to maintain control of a cat because it does not harm the cat if done properly, and it is effective in many cases. However, scruffing has become a controversial issue. Some cats react negatively to scruffing and actually fight harder instead of holding still. Also, some overweight cats have very little loose tissue to scruff, so the hold will be less effective.
In general, scruffing should be used only if minimal restraint techniques are not working. If scruffing seems necessary, try it for a few seconds. If the cat gets worse, discontinue and try something else. When scruffing a cat, use the minimum amount of force necessary and take care to avoid injuring the cat's neck. A cat should not be lifted or suspended by the scruff because this is uncomfortable and may make the cat's behavior worse.
(Joanna M. Bassert & John A. Thomas, Clinical Textbook for Veterinary Technicians, 8th Edition, McCurnin's 2013, ISBN 978-1437726800 — p.186.)
‘Scruffing’ is a general term for a variety of holds on the skin of the cat's neck. Grasping the scruff of the neck varies from a gentle squeeze of skin, to grasping a larger fold of skin with varying amounts of pressure. Consideration of natural feline behavior can help put this technique into perspective. Cats grasp the scruff of the neck of other cats in only limited circumstances. During the first few weeks of life the mother cat may lift kittens by the scruff of the neck using her mouth. This is a method of transport and immobilization, and not a form of discipline. During mating, the tomcat grasps the scruff of the queen.
Some veterinarians and veterinary behaviorists do not use scruffing and do not condone its use. They find that using other gentle handling techniques is less stressful, more time efficient, provides greater safety for personnel, and allows the cat to have a sense of control. They prefer other methods to manage situations where feline welfare or personnel safety are at stake.
Other veterinarians handle cats gently and use scruffing only if it is necessary to protect the welfare of the cat or for the physical protection of personnel. Still others think that scruffing a cat is acceptable for short procedures, in an emergency, and to prevent the cat from escaping or injuring someone.
If you think this technique is the only alternative, carefully evaluate the cat for any signs of fear or anxiety. The cat may become immobile but may not be comfortable, or may become aggressive. Handle the cat as gently as possible and guard against using aggressive handling techniques out of anger or frustration. The panel does not condone lifting the cat or suspending its body weight with a scruffing technique because it is unnecessary and potentially painful.
(Ilona Rodan et al., AAFP and ISFM Feline-Friendly Handling Guidelines, Journal of Feline Medicine and Surgery, Volume 13, Issue 5, May 2011, Pages 364-375, http://dx.doi.org/10.1016/j.jfms.2011.03.012.)
Having a sense of control, even if it is not exerted, makes the cat more comfortable and reduces stress. Importantly, using the minimal amount of handling gives the cat a greater sense of control, so the cat is less likely to be aggressive.
Most of us have been taught to scruff cats, but scruffing often only increases a cat's arousal and fear, because scruffing removes the cat's sense of control. Many cats become fearfully aggressive when scruffed in an attempt to protect themselves. Some veterinarians, especially in Europe, find “clipnosis”¹ helpful for restraint. This procedure is also controversial, again because it removes the cat's sense of control. In the author's experience (at least 5 years without scruffing or clipnosis), cats are usually calmer and easier to handle if they are not scruffed.
(Ilona Rodan, Understanding Feline Behavior and Application for Appropriate Handling and Management, Topics in Companion Animal Medicine, Volume 25, Issue 4, November 2010, Pages 178-188, ISSN 1938-9736, http://dx.doi.org/10.1053/j.tcam.2010.09.001.)
¹ IIUC, clipnosis consists in pinching the scruff of the neck with a clip in order to induce behavioral inhibition — hence the term "clipnosis", deriving from "clip" and "hypnosis".
BTW, thanks for asking, I didn't thought about such behavioral implications.