Not sure what the real life explanation is, but I would imagine any large interstellar alliance would have a single language that everyone would be taught (in addition to various species learning their own native planets languages).
As we saw, each species still has its own language even in the 32nd century... so it stands to reason that if they were UFP members, 'Standard' would be taught as part of their curricullum.
'Standard' may be very difficult to learn for some species within the Federation (I imagine a Brikar would have difficulties, for example), and learning it to a sufficient degree as to be able to communicate is not a half effort: you still have to speak/hear/maintain the language (whereas the UT is so incredibly convenient and everybody has so much other things to learn with the vast knowledge base of the Federation).
As an example of a large alliance lacking a single language that everyone would be taught: in the EU, comparable in some (not all) respects to the Federation, this is not the case. I'm not sure to what extent it is true in another large alliance that is in some respects comparable to Starfleet: NATO. I don't think every NATO soldier/specialist is required to know English, not sure about officers. I think it is probably restricted to certain categories, like military pilots. A tank commander in, say, Poland, would not necessarily be able to speak English even though that this is certainly the main language of that alliance.
And not everybody in the EU speaks either French or German (let alone both) to the extent they can actually communicate in it.
Learning languages is hard, for most (maybe all) people.
Its possible the holo showed more things that we (as observers) didn't get see.
Who knows.
Its also possible Gwyn went through the recording more than once after regaining her memory (she certainly did go over it to show what happened in the holodeck with her father).
Its possible there were elements to the holo that we just didn't see.
Yes, it's very likely Gwyn saw something that wasn't shown on screen, to us. But the point remains that this tiny star cluster (as it would be in the sky of Solum) wasn't at all highlighted in the holosimulation, unlike the twin moons that Soji saw. And that she would have to recall it from memory at Starfleet HQ (we can assume the hastily created shuttle did not have a copy of the holorecording), in order to distinguish it from all other star clusters that may vaguely look like it.
Along with her incredible ability with languages, and the telepathic/telekinetic properties, It's still a clear indication - IMO - that Vau N'akat are on another level as far as their fysiology (maybe this is the wrong word, but I hope you get my meaning) goes. Vulcans are standouts among prominent Federation members, with several abilities not seen in humans and probably Tellarites and Andorians, but even they seem to be significantly less developed as a species in certain aspects.
Both Ascencia and The Diviner have used the word "primitive" to describe other species or the UFP alliance, and while obviously not true in every sense, their feeling of superiority may be coming from the apparent discrepancy in the abilities that they demonstrate vs the average Federation denizen, as well as their apparent progress with AI/IT tech and protomatter. And thus not quite be as delusional as it sounds at first.
- So the Weapon can take complete control of Starfleet ships. Except for the one it's on apparently. Why did it allow itself to be taken away from the battlefield?
- The kids drifted aimlessly on a shuttle for a month and then crashed right in San Franciso next to Starfleet Academy without being intercepted by any orbital Starfleet resources?
- Gwyn bailing to help her planet kind of makes sense. She wishes to honor her father. The Unifier, I liked it.
The weapon: as crazy4xmaslights noted, the Protostar was supposed to be crewed by Vau N'akat who knew what they were doing. So the weapon will hesitate to sabotage the tools they should use, perhaps not helped by the presence of an actual Vau N'akat on board (the weapon may not be intelligent enough, or not be programmed to distinguish if this Vau N'akat is going with the program or not). It also wouldn't want to do what it did with CR721, because a series of malfunctions would make it impossible to use the ship further.
Crashing in Frisco: I guess this is an ST4 homage on the one hand, and an attempt to sell copies of the tie-in novel that has been announced (concerning their month-long journey with the barebones shuttle) on the other hand. For the episode it's a misstep, but it doesn't change much if they were just picked up near the Sol system by a starship, so we can let it slide as an homage that doesn't really make sense but does not really detract from the story.
Gwyn does not so much wants to honor her father (though it being his dying request does add to the pressure, I suppose), as she wants to save it from the apocalyptic vision of destruction that her father "divined" to her. Which is an enormous task, and one she said in S01e18 she never asked for. However, Gwyn does have tools in her arsenal that other Vau N'akat lack: knowledge of a realistic and very bad outcome for the future, knowledge of the Federation and other alien cultures/alliances/empires/threats, a working relation with Starfleet (at least I hope so!) and a clear tie to the Diviner (who will be around in a much younger version, and hopefully she will be able to reach him and communicate with him, both verbally and through her built-in bluetooth telepathy). It's a real shame she will have to do it all alone though (with the possible exception of some Starfleet support, but we'll see - why was Dal, at least, not sent to accompany and comfort her?).
