The Feds are paranoid about genetic engineering for "improvements" or major changes, but it appears they're ok with genetic tinkering to correct genetic diseases. Not sure how the Vulcans fit into this; they trot out IDIC, but they sure don't engineer *themselves* to be very different. Hell, they mostly all have the same *haircut.*
You are right to point out that the language used is a "Lingua Franca".
Despite what characters like Picard say, religion is clearly still rampagingly popular in the 25th century. The Bajorans and Klingons, for example, are blisteringly religious; and while humans don't seem all that demonstrative about it, there are clearly still a bunch of human religions. If "tribal" faiths such as Chacotay's are still out there, it's a safe bet that there are Catholics and Mormons and Hindus and such.
So we could safely assume that Federation is not fond of -
[Assuming an afterlife] Now you have L. Ron Hubbard spinning in his grave.
...And the Federation scientists immediately invented the way to turn dynamo with Hubbard rotations, thus finally making him useful for a change!
Probably a lot of AI priests.
Lower Decks are a very rare case of loving desconstruction; they make fun of cliches and weak parts of original, while respecting its spirit.
Not being willing to die and fearing death is a different things. I admit, that the borderline is relatively thin, but essentially it could be drawn at rationality. If someone is willing to do anything to get even a totally false hope of avoiding death (like giving his money to strangerly dressed men, who sprout nonsence about talking snakes, winged wheels with eyes, ect.) - then he is fearing death to irrational, instinctive degree.
The idea is even more dangerous for mounted units. In 1937 the mule that my father was riding was upset when he was wounded and threw its rider who fell backwards on his rifle. By incredible luck, Artillery Sergeant Manuel Miranda fell into a deep stream and lived to procreate.
Proof of access to an afterlife that looks desirable.
The second and third is essentially our attempts to rationalize our own mortality, born out of self-preservation instincst of primates. Since we did not exactly have instincts, but still have self-preservation fears, we attempt to rationalize them into existence of afterlife. And religions discovered that it's a great way of getting into other peoples pockets, by playing on their fear of death. No pockets to steal from (i.e. a post-scarity future) - significanly less interest from religion to play with people's fears. And if religions lost interest in scaring peoples, it would stand to reason that peoples would simply outlive the fear itself.
Post scarcity doesnt mean no pockets. Replicators cant make land, for instance. Or provide services. There will always be an economy.
The universe of Star Trek is DAMN scary,from mundane threats like Klingons and pirates to Borg, Doomsday Machines, Vger, space "gods" of all kinds, other universes invading, time travel warfare, etc. Religions will find fertile ground.
Now that you list it out like that, Star Trek seems like a very "Roman" setting.
Transporter accident
I suspect there are laws against just that sort of thing. Plus: we only see the episodes that feature "successful" transporter cloning. Perhaps, just offscreen, transpo-clones are an hourly occurrence, but they virtually always result in the clone not being just messed up, but horrifically so. Imagine the transporter accident from TMP was a regular result when someone tries to make a clone.
There is a significant difference between "not thinking like you" and "actively wishing for the destruction of your existing society"
Possibly like one of John Portman's atrium hotels. This is the San Francisco Hyatt Regency.
