FWIW, if I was a tandem dealer -- and I'm not -- I would NOT recommend discs to most clients. As a dealer, the last thing you want to deal with are customer issue's after the sale.
While I'm a strong advocate of the discs, just as I'm an advocate of S&S couplers, I recognize that they are what I'd characterize as "enthusiast" items that may not be appropriate for the average tandem buyer. Both options demand a certain degree of mechanican aptitude relative to maintenance and use. Lacking that mechanical aptitude, the average tandem buyer -- or a high-maintenance enthusiast -- will likely have questions that need to be addressed and will direct those to their dealer, often times in the form of a complaint that has already been shared with others. Both of those things are bad for business.
So, yes, I would agree with the mechanic at Bicycle Outfitters... disc brakes can be a PIA, particularly if you sold a lot of tandems fitted with a Formula disc to a lot of average tandem buyers. Similarly, the same would be true of the Avid's which aren't "perfect" out of the box and that will occasionally need some informed maintenance. And, as for travel, if you didn't have the fore thought to take some care in protecting your disc rotors when packing an S&S tandem I would also expect the rotors to be bent and wouldn't be surprized if there was some other related damage to the frame pieces or components they were pressed up against in the luggage.
Again, certain options just aren't appropriate for the average tandem team due to their complexity. The same is true of certain, lightweight or high-performance options that were originally designed for competitive applications which when fitted to the average tandem merely become something a dealer must address in the future.