The reality is anyone but Biles could be the alternate and the team would still be overwhelming favorite for Gold. So it comes down to the numbers and building the best team.
Only 2 from team USA can make each event final. Biles, Carey, Lee, Eaker are all reliably top 1-2 on an event or events.
So it comes down to Skinner vs McCallum, neither are top 2 on anything. So who better helps the team in team final where top 3 scores count? Losing Skinner only loses her vault, she is not top 3 on any other event. Losing McCallum means losing her bars. Skinner as alt means McCallum will do UB/VT in team final. McCallum as alt would mean Skinner vt/Eaker ub in team final. The McCallum combo is a more reliably higher set of scores. Her vault is strong, only about 3 tenths lower than Skinners. McCallum can also be used reliably on every event(she is around top 4 on EVERY event).
Skinner's best chance of making the team was proving she is better than Carey on VT/FX, and that didn't happen. The floor didn't get there and the Amanar didn't get consistent enough. But the progress by Skinner in short amount of time(on every event) was extremely impressive.