Only way I can think of to possibly combine the 2 would be through php. If it is possible to pass the htpasswd through a URL parameter, both logins could be done through same php script (would still be separate logins technically speaking).
I am in a very similar situation, except my users authenticate with Active Directory on our intranet environment. It would be really good to hear from you if you ever came up with a solution ... It's a pity PHpBB doesn`t offer an administrational option to choose your own login method.
We website currently uses phpBB and is bridged to Coppermine so there is only one login. I am now adding a document management program (OWL Intranet). All operate under MySql, but can add the phpbb login to the Owl.