undefined> It represents an approach to Star Trek that was cut off far too early, one that solves or avoids the most obnoxious pitfalls of the later seasons, and one I desperately wish we could have gotten more of.
I'll comment on this most important concluding statement with agreement. Ultimately, Discovery tried to do something different and did it fairly well. It's downfall was in not being willing to take that kind of storytelling and really lean into it. Fans started talking, loudly, about changes that were made and as a result later seasons of Discovery become far more tempered. The Discovery of season 1 could have ended Season 2 by sending Burnham and Discovery to the future and introducing a whole new cast of main players in a whole new context. Instead of that, they responded to the valid criticisms of the weaker supporting characters who don't seem to have much to do and as a result the show took a much more emotional turn. They haven't abandoned these long arcs, but they've tried to tell that story in a more familiar way and in my opinion this was always Discovery's downfall.
He was not under investigation for being genetically modified. I think a key aspect of this episode and that episode is that Julian and Una were both under investigation for concealing their status as genetically modified. Neither of them faced any penalty for having the modifications done.
It is only Mr. Bashir who is punished for seeking out and obtaining genetic modification for his developmentally delayed child. Being genetically modified isn't a crime and I don't think it was ever depicted as such - but having a genetic modification done is a crime. And having one done on you prevents you from joining Starfleet in some cases. Although for all we know Ilyrians are given exception to genetic modification rules as long as they're honest about it, but no human has ever gotten an exception so Julian lied to protect his parents and to ensure he'd get into Starfleet.