I'd be happy with a pair of large panniers - so an extra 8 to 10 inches of extended wheelbase should be OK. If an xtracycle bike would have 30+ inches of chainstay length, my plan would be to go 22 to 25 inches - this brings the BB to the center of the wheelbase.
I also want front suspension, and plan to use standard (26") MTB suspension forks with 20" wheels, and use disk brakes.
My initial plan is to use the Be-Bike Haze frame as a template, at least for the front of the bike:
Keep the geometry for the front of the bike intact, build an extended rear with an integrated rack, and find a way to break apart the front triangle for easy transport.
Here's an illustrated guide to what I want to do:

This shows the bike broken apart. The fork rests on top of the looong seatstays, while the rest of the front triangle falls to one side of the stays. The rear rack can be built wide to accomodate the front triangle. The front wheel is strapped to the side of the rear triangle. Skate wheels are shown attached to the rear rack like a brompton.

There are a couple of concerns. A bashguard should be sufficient to protect the chainwheel during travel. disk brakes will give good stopping power, but the rotors might get bent during transport.
The budget is also a concern. Since there's a definite small budget to the custom frame, I don't think I can go with S&S couplers. I'm thinking the ritchey/dahon system might be easier to replicate, or maybe copy some other coupler that uses bolts instead.