I've built and packed up a handful of tandems with both coupler arrangements. In general, I find having couplers in front of the captain seat tube to be the superior approach. However, some tandems can't be made to fit into an S&S hardcase with that arrangement. Here are the pros of of the front-of-seat-tube couplers:
1. Small head tube / front triangle: very easy to fit in case without fork. Sometimes possible to leave fork installed.
2. (as others have noted) Bike can be partially disassembled for cars/trains without adjusting the sync chain/belt. We occasionally put the tandem inside our hatchback by disconnecting the cable splitters and front couplers. Wheels, seats, fenders, etc all remain installed.
3. Reassembly of the frame tends to be easier.
Cons of loose tubes:
1. Loose tubes can be installed at any orientation or flipped front-to-back. Bottle cages or cable guides could be located incorrectly. For those bikes, it's handy to put some match marks on the couplers.
2. Front triangle and rear triangle are both very large chunks. It can be difficult to nest them together.
Pros of loose tubes:
1. Allows tandems with especially long stoker compartments to fit into S&S suitcase.
In both coupler arrangements, a captain crankarm sometimes has to be removed or reversed.