This was an excellent finale (as all four of them have been, not at all a given with modern Trek or frankly modern television in general), and fully justifies the somewhat weaker setup episode before it.
"A paywall on a bomb?" might be the best joke this show has delivered in it's whole run. I don't often crack up while watching these episodes, but this one really got me. At the very least it's up there with "It's a bomb! You can only use it once!" from Wej Duj. I'm sensing a pattern.
In more typical lower key Lower Decks humor, Boimler and Rutherford arguing about if Locarno looks like Tom Paris was excellent.
I do wonder what the plan is with Tendi. We've seen supposed major shakeups like this dropped into previous finales, of course, with Boimler leaving the Cerritos for the Titan at the end of season one and Freeman getting arrested at the end of Season 2, which were quickly reverted in the first few episodes of the subsequent season. Odds are that's the play here. I hope so, because losing Tendi would suck. She's a delight.
Why was Boimler the acting captain when the command staff took off on the captain's yacht? There was a full Lieutenant right behind him on the bridge, and surely tens of others on the ship who are more senior and more qualified. A little bit of a main character boost there.
I asked the same question out loud to myself when I saw Boims in the captain seat. Best guess: since the plan was just to tow the destroyer and throw it, they knew he wouldn't have to do much, and it'd give him a shot. Plus they might have taken his relationship with Mariner (and his rapport with the rest of the Lower Decks gang) into account. Lastly, it might have been a tactic for if the admiralty went through with court-martials. Whomever answered that hail in the captain's seat would be in more hot water than the rest of the crew.
Star Trek does this thing where formal rank isn't actually as important as being in the captain's in-group. Can you name anything important that provisional Lt. JG Ayala did on the USS Voyager? I sure as hell can't, but it was less important than Harry "eternal ensign" Kim.
As much as the Lower Decks gang would like to think of themselves as unimportant, they're very much confidants of the Cerritos' senior staff so it's illogical, but consistent for Boimler to be at the top of the list for acting captain when stuff's going down.
Out of universe it's obviously a narrative/screen time thing, I'd say you've just got to accept it and move on.
I'm pretty sure he was also the only command division officer on the bridge after they gave him command. At least in theory, due to differences in training, a lieutenant jg from the command track may be better suited for acting captaincy than a full lieutenant from science, especially with a decidedly non-sciency mission like flinging a warship at a wall. You need that dash of crazy that Starfleet's command officers tend to have.
It's also important to note that our LD crew are all bridge crew. We've seen that they have shifts at the helm and engineering/science/ops stations regularly, so putting them in charge really isn't that big of a stretch if the senior staff need to be off-ship for the more important role of the mission. They're basically babysitting the Cerritos and fending off hails from Starfleet.
The Tendi thing is basically the same move SNW made with La'an. It'll be resolved in the s5 premiere.
I did wonder why so many LJGs were on the bridge and why Boims got the chair, but I just chalked it to the usual - the otter more senior staff were up to something more important we didn't need to know about. Though it's certainly not unprecedented to give promising young officers the chair even when more senior officers are available. I take that as just part of Starfleet's training protocols.
The Tendi thing gives them options. They can do something with that next season, or just revert to the norm if they’d rather have her back with the main cast.
He is command track the other officers were engineering or security etc.
Maybe not "acting captain" but certainly I have seen equivalent in the merchant navy of a lower bridge officer being effectively in command of the vessel including more senior engineer