Yeah, this seems like another classic case of underestimating the demand. Tome of Horrors Complete is another recent example, but it's hardly a new thing in gaming circles--Player's Handbook II for D&D 4E was awfully hard to get when it first came out (the .pdf policy changed around that time too, so there were a lot of 4E people in my neck of the woods that were not pleased).
It looks like the .pdf and the forthcoming print-on-demand format are the options for "the masses" that didn't get in on the pre-order. On the other hand, I personally know people that deliberately ordered extra copies specifically to put them up on eBay. It wouldn't surprise me to learn that perhaps a FLGS or two also ordered copies to sell as a "prestige item" in a display case or something. While I doubt that the secondary market will be flooded with extra copies, you'll see some go up on the secondary market when they ship out.