So what about genetic modification?
Swapping "unruly" with "docile" in a species is by that logic effectively the same thing, isn't it?
Basically the only way you can avoid doing something dystopian would be never to modify a species.
To summarize from both your posts - yes, in principle this is the same thing. Genemodding your species to alter their behavior, desires and capacities for your benefit is dystopian.
There's a substantial difference between "I changed my mind about X" or "I no longer enjoy X" and "I no longer enjoy X because I was deliberately altered by a third party so as to no longer enjoy X/change my opinion about X."
There's at least some degree of consent here, where if you agreed to it, it ceases to be dystopian. Agreeing under threat for Cybernetic means Cybernetic is always dystopian, because even if we then say that EVERYONE does agree to modification, agreeing "or else" is dystopian.
For Synthetic, the same problem is largely repeated. It's an even more fundamental change that entirely erases your original species in every respect, and there is again an "or else" qualifier to the idea that your entire population agrees to the change.
For Genetic, as well as general genemodding, there is not narratively an "or else" - both because tradition texts don't have anything so severe as "there is no room in our society for the group that won't exist in our society after we do this, but does before," and because you actually DON'T have to genemod inherently to use the ascension. Or didn't before, anyway, I haven't played 4.0 yet.
The inherent effect of Genetic was to do... absolutely nothing, actually, and there's no alarming flavor text really contradicting that, so it isn't necessarily dystopian. It's definitely not ruling it out, but it isn't inherent. You can either assume literally your entire species agreed to it (importantly, NOT under threat) or that anyone who didn't is abstractly "present, somewhere" still. Or just not use genemodding, which was basically not worth the project costs a lot of the time before anyway.
The inherent effect of Cybernetic is to declare that not being Cybernetic is unacceptable and make your entire species Cybernetic. That's
extremely clear-cut. There is no choice, at the absolute best interpretation the pro-Cybernetics side is saying "well due to our changes you'll die unless you get Cybernetics." Even if everyone then does, that is dystopian.
The inherent effect of Synthetic is essentially the same, slightly toned down rhetorically actually, but with even worse actual pop modifications.