I want to push back on the conversation between Jack and Bashir in "Statistical Probabilities" a little bit given additional context from Strange New Worlds "Ad Astra per Aspera." I don't think it's fair to say that all augments are treated the same way. It's unlikely I think, that even if Bashir were to have not lied to get into Starfleet he would have been prevented either by law or by policy of doing anything even remotely scientific - including medicine or other gene research.
However, I don't think we can take Jack at his word that he would have been institutionalized in the same manner. If we believe that the genetically modified people we see from the Institute in Deep Space Nine weren't driven mad by their perceived incarceration then we have to believe that side effects of the genetic modification process caused unexpected neurological abnormalities and personality disorders that we see typified by that group.
Dal, for instance, in Prodigy does not fear institutionalization in the Federation, but rather he fears he won't be let into Starfleet. Presumably he may also be precluded from other career choices that he's just not interested in, but I don't think it's fair to say that being an augment is criminal as much as it is laws have created a system whereby modified people, especially modified humans, are treated as second class citizens. This might even extend to people who have DNA sequencing done for legitimate medical reasons like Chakotay. I like to imagine Chakotay and Una and Bashir having similar experiences even though their circumstances were unique. The human willingness to look past reason and into bigotry doesn't go away, but it's focused on the genetically modified.
And it takes decades, centuries even, for the laws to change even a little bit and even longer for the people to accept those changes.
Whoa! Good catch. That timeline almost lines up exactly and it's very possible that O'Brien was referring to Una. It could also be that O'Brien is indicating that sentiments have maybe changed somewhat in 100 years, something that we are lead to expect from SNW. And indeed Bashir is allowed to stay in Starfleet without even having to find a technical loophole and Richard's punishment is considered harsh at 2 years. Given the future utopia that we're dealing with and the historical significance of the crime I think what we're seeing is that no one really does this anymore and so it's not really an issue.
I really hate that Prodigy was unrewened because a courtroom episode of Prodigy where Dal gets the right to serve in Starfleet and the Starfleet ban on genetic augments is lifted would be a pretty cool.