Prasun, given the timing of our mutual interest in the pile of fail that is Duo, I'm guessing we may attend the same large midwestern university. 

Different schools, but similar problems. All the more relevant I guess since large universities are deploying Duo. I mailed Duo regarding technical documentation, and they said that their app is the only supported way, which is not surprising. If someone has the ability to contact someone higher up in Duo, that would be really helpful.
All the same, I'd rather spend my energy trying to convince IT that they should enable token types that are based on public cryptographic routines combined in standard ways than on trying to reverse engineer the proprietary Duo token type so we can emulate it in FreeOTP. That's better for the school, and keeps FreeOTP from being in a position of trying to maintain compatibility with a proprietary application with no published specifications. (At least, none I have found yet.)

It may be the case that Duo uses HOTP internally, but with some closed parts around it (such as the the phone home parts that you mentioned earlier). Convincing either Duo or universities to do something differently is likely not very easy.