I just wouldn't even contemplate getting a rim brake tandem these days unless you were trying to build one that was ultra light and every gram counts.
As to the weight difference between disc and rim brakes if you are riding lots of hills, with rim brakes you would need to use a drum brake as well. The additional weight of a drum brake when you add it to the rim brakes will most probably be more than just disc.
Using disc brakes means it's an easy swap between 650b and 26" wheels.
I would be suggesting that you find another builder. We have a custom Co-motion Mocha with S&S couplers and 26" wheels (ours will be 13yrs old in a few months so bought before 650b was a thing) that we've been very happy with. We required a custom frame do to a 11" height disparity between myself and my lovely stoker