I happened to read the test of the DCT in the current issue of Sport Rider in the store the other day. The commentary (I would assume this was the message from Honda) was that in the DCT the dual clutch basket is not quite as robust as that of a single clutch. Kinda makes sense since they are essentially stacked on top and concentric as well. The added 2 inches of width means the huge forces it must transmit are extended farther outbound on the coaxial shafts and clutch basket fingers, my intuition suggests it would not be as structurally sound as a thinner, more compact basket mounted on a solid shaft. This is not to say the structure is weak, but every component no matter how strong still has it's breaking point. Honda being traditionally conservative probably chose to err on the side of restraint and added reliability over all out performance.
That said, it does not explain why the same crippling in the first 2 gears is present on the standard clutch model which does not suffer the same mechanical concerns unique to the DCT. It could be that for the first year out they want to be conservative with both models to gain some real world reliability data, and perhaps dial back the degree of restraint in subsequent releases. Dunno why, but you have a good point that Honda (and virtually all companies) certainly has their rationale for the engineering decisions they make. The last thing any manufacturer wants is a massive design flaw that will cost them millions to fix. Just ask Aprilia about their RSV4 woes.