For what it's worth, we were down the first 10 days of June with two families from different parts of the country (one Orlando, one Phoenix). Each family did their own submission to the portal, using two separate emails. This was needed for us for some of the same reasons you outline....different travel times, different testing times, and the need to comply with the 48 hour window.

We had no issues having the submissions separated, outside of the normal lag/delay in getting approvals from the portal. As others have mentioned, the most important thing is that each submission is completed with all required info from the outset. As long as you do that, you should be good.