Hello Eric:
Yeah, that kind of bugs us, too. The Project Board is the only board in the collection that we didn't design and make ourselves. The Project Board is sourced directly from the company that makes the sound chip. We've considered making our own version of this board, and if we do we would certainly fix the alignment so that all the holes are on 0.1" centers.
Foxonix - make your ideas heard.
@foxonixdev