Yeah it seems the system just performs a basic check on whether an account is active or not. When they designed the alpha application form they could not have predicted SE setting all accounts to active and just took the easiest route of coding a simple check on active/inactive. They may even be aware of the issue but deemed it too low priority to fix.
The decision to open the floodgates was most likely a late/last minute decision and since it sounds harmless on paper didn't go through the full testing process to find out what the consequences would be.