I'm pretty convinced this is not the original show's timeline, but that we'll end up there eventually. Maybe they'll set it up so that the events of this show become pivotal to the way things were in TOS. Think about the mysterious bird of prey flown by T'Kuvma and his group - it's the only one with cloaking tech and none of the crew on board seem to be scientists, yet the ship is clearly of Klingon design. More like the birds of prey we're used to seeing. So where'd they get it?
We already know from TNG and DS9 that to regular people living in the Federation Starfleet and its officers have a squeaky clean, Boy Scout reputation. Despite the no-money theme of government service we know other people (including humans) engage in commerce. There are shady businessmen, even organized crime syndicates. And the Federation government itself has a dark side. The agency Section 31, which was written into a classified part of its charter, whose oversight is unclear - maybe even nonexistent. They do all the things a covert intelligence division would be expected to do. Conduct surveillance and infiltration, recruit civilians to help them, even conduct assassinations or other attacks that one might consider terrorism, all supposedly in the service of Federation interests.
There's always been plenty of the grunge of real life in the ST universe. It's mostly not been a focus, although DS9 and Enterprise showed more of that stuff than the other franchises. Credit advances in special effects for the fact that current sci-fi shows often feel more like actually being there and less like movie sets. Granted there is a conscious effort with Discovery to make the mood darker with a hint of looming menace. Including a captain who's slightly unbalanced. Or maybe more than slightly, we can't really tell yet.
Interesting observations. I actually liked the most recent episode more than previous ones.
Could be just a case of warming up to the new Zeitgeist.