I know of two solutions to your question - I'll post two brands, however they are not meant as an advertisement, rather as a starting point for further search.
One is used by Onderwater Fiets from Amsterdam. Their tandems (and also more persons bikes) combine the stoker and pilot function and are meant for families. There, the drive is permanent between the last bottom bracket and the rear wheel and other bottom brackets are somehow free-wheeled so the passengers in front can pedal individually.
The other is R&B Fly, not much can be found about those on the Internet. Funny thing, I own one, hence the independent drive can be further inspected. There, each chainring (single for the pilot; double, same size for the stoker) attached to the crankset is freewheeled, thus pedalling can be done independent. Anyway, this bike awaits some renovation, I haven't ridden it yet.
Thus, it is possible to build a tandem with independent drivetrains and with enough invention you can even build one where the cadence don't need to match (add a front derailleur and triple chainring to the pilot's seat for higher / same / lower cadence as the stoker).