I strongly urge that accommodations be retained for a stackable project board by gathering unused / important control lines as well as the power lines to through-hole header layouts. There are several headers in the Alpha boards; whether or not they stay in on a size-shrink final version is TBD, I think.
Remember what made the original IBM PC a legendary hit: the ability to plug in third party add-on cards into its ISA bus, a concept still in use 30 years later in the x86 machines. To make the Rpi an equally legendary hit, you must allow for hardware expandability with stackable boards that fit its form factor.
Currently you have some headers on your Alpha board but I seem to recall reading that they were going to be removed in the size-shrink final version after using them as test points during debug. I sure hope not. Those headers are the key to expandability.
I would propose that not only should you have a through-hole header layout, but that you do not populate it on the final board. Several reasons. First, it saves cost for an additional component that most users won't utilize anyway. When you DO have a tinkerer come along, they will then have the option of soldering the header onto EITHER SIDE OF THE BOARD. Having the header as you have it in the Alpha board is actually very space inefficient - it is on the component side, so using it as an expansion path requires a LONG header and board spacers that gets the expansion board above the components. Better to put it on the smooth "bottom" side where only a small header is required to get "above" the SD card slot mechanism and only a few washers would be needed to support the board.
Alternately, if you DO populate the header, I recommend making sure that it is sized so that a mating connector on another board can fit into it and still clear the components on the Rpi. Preferably you should have a specific through-hole connector in mind for such a purpose that you have verified the fit and component clearance on, and be able to provide its part number thru DigiKey or some other vendor.
Bottom line, including an empty through-hole header will provide a starting point that will jumpstart a BUNCH of add-on board projects. Surface mount may be the key to affordability and size-shrink, but through hole is the key to getting tinkerers involved in actually making a variety of custom add-on boards.
IMHO, an easy route for a stackable project board for the Rpi is a custom PCB from ExpressPCB. I have used them for many projects and they are AWESOME. They do three copies of a custom double sided 3.8 by 2.5 inch fixed-size PCB (96mm by 63.5 mm) for only $51 (around 30 GBP) with 24 hour turnaround. This size is exactly in the ballpark for the size a Rpi stackable expansion board needs to be. Plus ExpressPC has free downloadable layout software that does everything you could want it to do, another plus for open-source sharing of stackable expansion board ideas that could start from a universal mounting hole / header hole template. They ship international to the UK and elsewhere. Highest recommendation.
http://www.expresspcb.com/expr.....iboard.htm