As others have said here - visas are issued by the Ministry of Foreign Affairs and (according to my missus who works for them) no checks are made by embassies and consulates before visas are issued.
One suggestions here is to buy an air ticket, then see if APIS rejects your passport, telling you to do it at the airport check in, when you try to register it and check in online, . You'd need to know which databases APIS checks to be sure of that though.
Hard to get a definitive answer on that one, unless you know someone who works in the right part of immigration.