I have to say, I kind of like the idea of a darker, more insular Federation though? If we go by DS9's ending pretty much every major threat is done with. The Alpha Quadrant is near unified but with shakey diplomatic backgrounds and the Federation has either neutralised most threats or bedded them down to the point it would become very insular.
I think the key difference was that DS9 understood that the best way to make an inherently optimistic show darker was by putting Good people in bad situations; not making your "heroes" assholes that are slightly less messed up than the villains.
I don't doubt Sisko is every bit a good person as Picard is, but you could feel that what he did to win the dominion war pushed him to the edge. I think the key difference between the two is that Sisko wouldn't doubt to sacrifice his conscience if it meant saving lives, while Picard would never sacrifice his morals even if that had meant they all would be dominion citizens by now.
There's a very good reason section 31 was so secretive, besides them being very good spies. Kurtzman is trying to push a show for them, and have them as the cool and edgy group which is missing the point. While the Cardassians and the Romulans were proud of the Obsidian Order and the Tal shiar, In DS9 every single good guy in the federation was ashamed of the idea of section 31 even existing.
Hacks like Kurtzman's idea of "darker" is to just make the heroes depressed, drug addict assholes, which is fine for a 15-year old that thinks smoking is cool, but incredibly childish otherwise.
TL;DR the best way to make the federation darker, without compromising Star Trek's whole concept, was putting them in difficult situations not making them outright bad guys for a poor Brexit methaphor.
Also I might have misheard the dialogues but there are many copies of the Dahj/Soji model?
Yeap, apparently the captain knew yet another woman that looked exactly the same to Soji, for some reason.
Also... is it just me or did this episode feel completely disconnected from the last one? Why are Soji and Picard again back with Raffi and the others? Weren't they with Riker's family on their way to meet another captain after Kestra helped them?
The last episode before this one indeed feels like a last-minute addition, not that I'm complaining about seeing Riker again, but still seems like they just added the blue tracker plot to justify a detour for nostalgia that wasn't there in the first place.