Reading the BAA wording more carefully, I think only accepted applicants to the 2020 marathon will be able to apply for 2021, regardless of the aging up issue.
"Entrants who were accepted into the 2020 Boston Marathon by way of a qualifying time may use their 2020 Boston Marathon qualifying time to apply for entry into the 2021 event. The beginning of the qualifying window for the 2021 Boston Marathon has been established as September 15, 2018, which means that we will accept qualifying performances posted for the 2020 event into the 2021 race, as well."
It's not totally clear though that they won't open it up to others, there needs to be more clarification. The issue of people within the cohort of accepted applicants aging up is still there though... allowing someone two years younger to gain the advantage of a slower age group qualifying time isn't equitable. The BAA could say that your qualifying time will be determined based on your age as of April 20 2020 if you decide to submit a time from that prior period. But I doubt they will do that, and I don't think the BAA is concerned with equitability.