(You probably meant, Bradie and Alysa are *unofficially* our top 2 girls, given Alysa came 4th at nationals this year).
Bradie, as national champion, gets Skate America unless she doesn't want it (unlikely). Now, I'm still learning how the rules for GP assignments go, but Alysa came in 4th at nationals (as close as she, Amber and Karen were in 2-3-4), so I know there's no rule disallowing Alysa to be assigned to SA also. She's also popular, and you cannot tell me that USFS is not going to pin their hopes on her next season. She's not guaranteed another GP assignment because there was no JGPF last year and no Junior Worlds, so given that she needs to start accumulating points for her inaugural international season, she is 100% getting SA. (I have high hopes she will get another assignment though).
What I'm not sure about is whether the US Nationals placements means neither Amber nor Karen could get the third spot as SA. If that rule only applies to Worlds placements, then I'm inclined to think the third spot will go to Amber, as sort of a consolation for not getting picked for Worlds and so everyone can get a good look at her (because Alysa is definitely getting picked for Nebelhorn). If it is true that Amber and Karen can't take that spot if Bradie is assigned, then they'll give it to Mariah.
tl;dr: That rule only applies to Worlds placements.
Nationals placements don't officially (that is, according to the ISU's rules for the Grand Prix) have any effect on GP assignments. No skater is guaranteed a GP assignment based on their nationals results, and no federation is obligated to take the results of any nationals into account in its invitations. An individual host federation
could make its own internal policies about not matching up its top nationals finishers at its GP, but it would probably be ill-advised to make ironclad rules for itself, because there are all sorts of circumstances in which it would be desirable to make exceptions (for example, for skaters who break through and finish on the podium at nationals, but who don't have the World Championship results or the ranking on the World Standing or Season's Best lists to qualify for an automatic GP invitation the following season).
The ISU hasn't posted its usual annual announcement of the selection criteria on the usual spot on its website yet; AFAIK they haven't been released at all. But pre-Covid, the top 12 (singles) or 10 (pairs/dance) finishers at Worlds were each guaranteed two spots. (Of those, the top 6 finishers were seeded, so that skaters who finished 1-3 couldn't meet each other and skaters who finished 4-6 couldn't meet each other until the GPF.) Skaters who didn't place in the top 12/10 at Worlds but were ranked in the top 24 on either the World Standing or Season's Best lists were guaranteed one spot. Skaters who didn't meet any of those criteria, but who had a top 75 Season's Best score or a medal from Junior Worlds or a gold medal from the Junior GPF, were eligible to be invited to a GP but not guaranteed a spot. And there were provisions for skaters returning from a season off, changing partners, moving up to seniors. Who knows what they'll do this year. But as of 26 March Amber was 30th on the World Standing list, outside the top 24 who are guaranteed one spot – and of course, she has no Worlds placement or ISU Season's Best from 2020-21. So under the pre-Covid rules, she wouldn't be entitled to an automatic GP spot; USFS would have to pick her for SA to guarantee her a spot, and that assumes that they could do so under the rules. The ISU GP announcement for 2019-20 states that "The domestic Skaters/Couples should fulfil the criteria of being on the top 75 Grand Prix Season’s Best list when first selected" (pp. 3-4 of the document linked below), which is not the same thing as "must" fulfill the criteria.
Basically, USFS can choose any three American skaters with a top 75 Season's Best (and even that seems not to be an ironclad rule) for its spots, as long as the final results of the first round of GP invitations (before withdrawals) conform to the ISU's rules about seeding, guaranteed places for skaters high enough in Worlds placements and the World Standings and Season's Best lists, etc.
You can find the pre-Covid rules about GP assignments
here.