Actually only 5 got nominations, but still, it's 10% of the graduating class. All of them got a nom to at least 2 SAs from their Congressman.
Also, DD got the 2 noms from her congressman before she went to McCain's committee. The primary nom carries more weight, though, so it makes sense that she got that (as you said). It could be that the Congressman didn't share the information.
Good question about why she got the alternate to USNA when McCain's committee gave her the primary to USAFA. McCain has an 8-10 person committee that interviews each candidate, so I suspect that they break into 3-4 groups and put the lists together independently of each other. That's just my suspicion, though. Of the 5 kids that interviewed with their Congressman, 3 were chosen to interview with McCain. Those 3 got a letter from Flake saying that since they already received a nom from McCain, they were removed from consideration. I don't know if the other 2 got noms from Flake.