They still have to qualify for a spot in the final. And even if an individual only qualifies for a single event via the World Cups she's still allowed to compete the all around. So if Jade wins only vault in the World Cups she'd be able to make the finals on both vault and floor if she performed well enough in qualifications.
The real crux of this is that individuals still count in the 3 per country rule for all finals. Plus team qualifications are 4 up 3 count and finals are 3 up 3 count. So the people they name to the team have to have solid routines on all four events, one of the highest combined scores on three events, and (and this is the part Skinner may be lacking) the ability to be top two on at least one event to make the event final. The trick is, it does team USA no good to put a vault/floor standout onto the team when Jade's an individual because they risk ending up with two outstanding gymnasts really just competing against each other to make the final and not adding to their medal count. The US is pretty far ahead in terms of team scores and they're likely to have a lot of options with similar all around potential so it's going to be tempting to put up Simone, their number 2 all around (Morgan's looking likely,) and a pair of bar/beam standouts who can make those event finals. Again, I'm excited to see what Mykayla can bring to the table, and if her improved form in NCAA can translate to elite. She may very well have a shot. But sadly, she can be second in the country on both vault and floor and still not make the team if the logistical side of things doesn't work out in her favor.