Upon reading the duo documentation, it appears that there is some support for HOTP tokens and other third party devices such as the yubikey. Tokens can only be added by "Owner, Administrator, User Manager, or Help Desk" though, which will likely be impractical for most users since very few people, if any, in the support dept. will know about this, and will probably be reluctant to approve this even if the issue reaches the right level of authorization.    

On Wed, Jun 22, 2016 at 1:20 PM, Prasun Gera <prasun.gera@gmail.com> wrote:
 According to their web site Duo allows for the use of HOTP tokens, so there's probably not much benefit to reverse engineering their proprietary token type.

I think what they mean is that the duo app can support HOTP. i.e. The duo app can act as a replacement for freeotp or google authenticator. However, if your organization uses Duo, you are stuck with the duo app for now.