Obviously, our ship marks the time of day as though they are on Earth, and their regular shifts vary. (which is why in TOS the exact crew wasn't on the bridge all the time. Near exact, but not exact.) As for "night shift", Gene did state that the ship's lights dim overall during the late night to keep the crew and their biological clocks healthy. (If you've ever flown overseas the airlines do this too... going all the way to turning the cabin lights OUT and then throwing them on when they want you to wake up.) Now, whether that is carried over to the "working" sections at night - most especially the bridge - is worthy of debate in my eyes. (I don't know of any company where the 3rd shift reports to work and the lights are dim compared to the lighting the 1st shift works in.)
As for the over-all lighting, I think it's just an effect of being on YouTube. I only remember Jon mentioning it for the bridge, and our lighting team throws so much light we've popped jiffy pop off them for the whole crew between takes. If the high res and streaming versions released later strike you the same I would be surprised. The version on my hard drive looks great.
Middyseafort, our production is a "git-r-done" production. We look at what we have to do to get to the end product, and do whatever it takes. While they were filmed, we do not possess the footage of some key scenes that were shot and are needed for the story to make sense, and at least one key scene needs to be re-shot because it doesn't cut into the episode the way the director chose to previously shoot it. (We'd rather not discuss why we are missing the footage and would prefer others not belabor the point either. It is what it is.)
Two of the guest actors in these scenes have moved on to other things, so their parts have been recast and they will be replaced in the episode. The new actors are doing an awesome job from what I've seen in prep! (I'm not high enough on the food chain to release character names without prior permission.) It's nothing to be concerned about - when Ben Tolpin decided he no longer had the time to devote to Spock, he was similarly replaced in "Enemy: Starfleet". I bet you never noticed.....
The missing scenes/reshoots will take place in either April or May, dependent on funds and James' ever increasing work schedule/con appearances.