The cost difference between Co-Motion models is pretty much tied to the differences in the cost of the materials and labor so that extra $1,100 buys you what you've already identified:
1. A somewhat lighter weight Reynolds 631 air hardened frame that exhibits the same basic handling qualities as the Reynolds 725 heat-treated frame used on the Primera and the S&S equipped Speedster, Mocha & Supremo Co-Pilot travel tandems. Back in 2003 the frame-only cost difference between the Reynolds 631 and 725 framesets was about $350 or a 20% bump associated with the more expensive tubing. I'd venture a guess that adjusted for inflation it's probably closer to a $425 - $450 bump nowadays, but that's just a guess.
2. A brand-name component package vs. the value-based component package used to keep the price down on the Primera.
3. Your choice of 30 colors vs. standard silver or red Primera color options included in the base price vs. paying a $100 bump to level the playing field with the Speedster on paint finishes.
Therefore, the real question is... noting that you're already considering upgrades like the disc and suspension seatpost ...will you be just as 'happy' with the best-value Primera model as you would with the slightly more upscale Speedster? Frankly, there really won't be much of a performance difference aside from the ~1.0% total bike's weight reduction and an equally undetectable difference in the quality of the bearings used on the Co-Motion-branded hubs vs. the DT Hugi hubs. Therefore, most of the quantifiable differences will be oh so slight weight differences and the finish of certain components. Tires really don't factor in to the equation since they're consumables that will be replaced in a few months anyway.
So, what's your gut telling you here???
Will you and yours appreciate the added-value of those premium-grade components and that lighter frameset? Or, would you rather put that $1,100 towards your optional disc, a suspension seat post and a paint upgrade? It all adds up rather fast and, well, beware the cost of accessories for the new tandem and wardrobe enhancements that often times seem to follow the acquisition of a new tandem.
Enjoy the process because, on the bright side, I don't think you can make a bad choice so long as you get the frame size and color right, as everything else is fairly easy to change.