We're using the Avid BB7s on a stock C'dale road tandem and from what my pilot's tell me, they work very well. However, we spend a lot of time faffing with them trying to get them set up correctly and invariably end up just having to accept some noise - if not with the pads rubbing, then from the whistling which seems to be caused in high winds at low speeds as maybe the disc is slightly distorted by the wind.
We're a heavier team (350 lbs) and do a lot of climbing which obviously increases the wear on the brakes and amplifies the issue.
Having experienced similar issues adjusting rim brakes on another tandem, again setup with STI shifters like the C'dale, I would probably err with a dedicated long lever brake caliper with either hydraulic rim or disc, or mechanical rim brakes and bar end shifters which would allow a greater degree of tollerence for us, if I started from scratch for a training bike.
Obviously you wouldn't be able to use any of the integral brake/shifter systems but these generally just don't seem to allow enough movement for us and would spend more time on the bike if we weren't having to continually adjust our brakes.
One thing I heard recently though is that some manufacturers are now producing hybrid mechanic / hydraulic brakes, which I think involves a standard caliper and cable moving something in a resevoir at the braking end but this is only speculation. This could offer the best solution as you could use standard road levers / cables while benefiting from the self adjustment and hopefully increased movement of hydraulic brakes. Be interested to know if anyone knows any more about these or has even tried them.