A big part of what you're describing is just 'The Amish have a point', no?
I'm super confused, I'm a fan of transhumanism, and looking back at episodes of TNG and TOS now vs watching them when I was 9 it's just hard to not take all the sci fi and such I've read and look at Trek through those lenses.
There are "token cyborgs" in Trek, we're getting to the point today where an artificial heart is boring, lord knows they have the technology to put all the shit in that visor Geordi wears into a package that could fit on the head of a pin and just implant it into the replacement biological or cybernetic eyes which they could easily make for him, it isn't like it's plausible to assume they just started backsliding on processor technology, we can stick chips in an eye nowadays that can restore a significant level of eyesight, we should be reaching the whole "broad spectrum crazy analytical function having" level of gee-whiz gadgetry which the visor has within the century, except we'll be doing it with something like a mesh of graphene or silicene or something on the back of the eyeball, and besides the awesomeness of planar molecular structures, all of this technology was old school shit in sci fi.
Back in 87 Baxter published The Xeelee Flower, the roots of all the crazy godtech the Xeelee have, the exploration of human development and expression vs the later insanity as humans decided to beat these godlike and ineffable beings the only route was to make damn sure they remain completely human, locking their genetics down, banning augmentations, and breeding en masse to throw generations of child soldiers against the fortifications of a race that was fighting a war on a scale so large the humans never even noticed it.
I look back through the stories in the Xeelee Sequence and notice the similarities with a lot of things from the Federation and the Coalition/Third Expansion which are really unsettling. In the Xeelee books humans developed anti-senescence technology and banished death, until a neighboring species discovered how primitive we were and occupied the planet to make money, they made use of controlling the AS tech to keep people in line until things turned towards genocide, we poisoned the oceans (they were aquatic hive minds) to kill them, so they set up some crazy ass heat-sink system and froze the oceans solid to punish us. We finally managed to break loose and regain our immortality and freedom, helped by the tech which we acquired from our former conquerors and lived well, until another race caught wind of how pitiful we were, even with the stolen tech, and once again withdrew AS treatments, bringing back death, only this time after getting free they were inspired by a guy who insisted that humans are best when they are what they were during the occupation.
A brief life burns brightly....then you get Star Trek, for the most part they are waaaaay behind the Xeelee, but there is shit that Trek has that competes with magical alien godtech, replicators, cloaking devices, matter deconstruction/reconstruction, crazy force field tech, and then you're faced with a couple of explanations. They don't try to improve their bodies, extend their lives, and so forth because of anecdotes from all these other races that fuck shit up, so even given the technological prowess they clearly possess, and supposed rational and scientific outlook they espouse, they'd be better off leaving it alone.
...oooorrrrr, they're utterly incompetent and literally couldn't think of any of the numerous ways to apply their absurd tech level to make things better for themselves and others?
Still, there's one thing you can say for Trek and their fucked up priorities or incompetence: at least they never made a
handgun you could kill a star with!
Do note though: the Xeeleeverse is
depressing, I mean, it's cheery compared to Manifold: Space, but so's a trip to a holocaust museum, most goddamn depressing story ever, but Trek is supposed to be inspiring and cheer you up, "to seek out new life, and new civilizations, to boldly go, where no one has gone before!" and all that jazz.
Don't forget the 'problem' of transhumans like Khan Noonien Singh posed to the pre-Federation (and not exactly unproblematic to the UFP). And Dr Bashir had to keep a secret...
Oh god, yeah, I'm like straight up, more Montalbans/Cumberbatches running around isn't a problem... wait, you meant the character part didn't you? The Monalban Khan was charming and admirable even as he was casually discussing why it is in your best interest to just get it over with and submit to his whims, he'll treat you like a beloved pet, and it's easy to believe. The Cumberbatch one was angrier, but still had that rich rolling delivery and sense that he's already figured out which cards you're holding and knows you're trying hard not to kiss him, I mean not that I'd kiss him, I'd give him a hug though.
Sadly that's the only way transhumans get presented: sexy and scary bad boys like Khan or ultracompetent and powerful but utterly meek and emotionless dolls like Data. Can't have a normal transhuman, can't have someone who is just an ordinary dude that replaced 90% of their body with artificial parts, he's gotta be a battle scarred warrior left behind by his comrades out for vengeance, it's just weird and unsettling seeing people talk about it like it's a future to strive for.