With the end of season 1 in sight and with Dal's augment status (and what it means in the Federation) now in the open, it may be interesting to look at the possible implications.
Given that the ban of augments has been described by people from the production as "the last prejudice in the Federation", I'm guessing this won't be resolved as part of the season finale and it will get its own 10-episode or season-long arc before Dal may have a realistic possibility to apply for Starfleet. I'd expect that such a prejudice won't fall overnight after a good speech by VA Janeway, as it is not Prodigy's style to solve such problems (beyond the specific mystery/distress of the week) within one or two episodes.
I also think that it's likely that the Protogies will continue together on the Protostar during season 2, possibly involved in an attempt to rescue Chakotay and his crew. Which would also mean that the Vau N'akat storyline would continue in some form. And I would guess that they will be instrumental in saving Chakotay and gaining some sort of accomodation with the Vau N'akat, giving VA Janeway munition for their eventual admission.
I also think that Dal's eventual admission will not be framed as an exception that will be hushed over, like Bashir (and probably Una), but it will lead to a change in policy. I don't expect Prodigy to go for less than that.
The threat of the living construct will likely be ended or at least "paused" in the season finale, perhaps the Diviner shuts it down (though he may do so under certain conditions with the ability to activate it again should those not be met; he could for example demand that Starfleet does not make first contact with the Vau N'akat or he may get the Protostar and its crew to travel with him to Solum in the future so that they can see the results of the war there - if he can find the same or similar anomaly Chakotay ran into) or the teens and the Janeways find a way together.
As an aside, I think the unfortunate message of VA Janeway for Dal shows that Starfleet is too rigid. By refusing Dal, they also very likely miss the chance to get Gwyn into Starfleet. And while Gwyn's application could also present problems (due to her not being a Federation citizen, being complicit in slavery, attempting to steal a ship from Starfleet on behalf of the Vau N'akat, and potentially conflicted loyalty in future dealings with Vau N'akat), the others normally should be admitted pretty easily. However, Rok, Zero and Jankom may also decide that they can do without Starfleet if Dal is not welcome there, and even the most conservative/morally rigid Starfleet admiral would rue the loss of someone with Rok's enormous potential.
Moreover, they run the risk that the group decides to simply keep the Protostar even once the weapon has been neutralised, if they are not welcome at Starfleet, which would be a very bad outcome for Starfleet. Even if they don't, they would have Dal and Gwyn on the loose in or around the fringes of the Federation, probably looking to join some other organisation that would take them in without prejudices and restrictions. As they know confidential details of a very advanced Starfleet prototype, and both teens have unique properties (physiologically and genetically) that would make them potentially very interesting for less scrupulous organisations (like the Tal Shiar or Orion syndicate, for example), that could also end up backfiring badly on Starfleet in one way or another.
It's situations like this that show that organisations like S31, or other possible fringe divisions of the intelligence or operational branches of Starfleet that may be willing to be more loose with some of the rules, can have value. The best outcome for the Federation, in a hypothetical scenario where VA Janeway does not attempt or succeed in getting them into Starfleet, would probably be to lead the teens to a branch organisation that has (covert or open) Starfleet support, but that is not legally Starfleet and thus not necessarily subject to the same restrictions. Say, something like the Fenris Rangers or Lower Deck's archaelogists guild. Or indeed, S31 itself. They could potentially be very good "operatives" for S31, though I very much doubt a family show would ever go that route.
Having said that, I fully expect the show will get them all into Starfleet and probably due to the full support of Janeway and Chakotay.