I hadn’t read the guide on merging with wordpress – I am building it into a CMS built for a client.
I had already adjusted pluggable.php instead of simply editing bb-config and adding the cookiepath, d’oh!
I actually have a working solution now. Instead of ussing about with automatic login the main website can generate a cookie that BBpress likes. I did have to modify wp_validate_auth_cookie and wp_generate_auth_cookie to include my own hash and adjust the config as pointed out above but otherwise everything is unmodified… so far!