Thank you for the reasonable and logically backed up answer, xander. However, I don't feel it would be such a hit to Bit Blot's bottom line as you make it out to be. I know Gish from Chronic Logic allowed you to run the game from any of the three platforms after purchasing your registration key, and that game ended up making good money. And I expect Aquaria to make even better money than Gish.
So Chronic Logic have decided to make that possible. IV have done the same thing with the Linux and Windows versions of their games. And more power to them -- I think they are doing a good thing. Also, note that I haven't a clue what Bit-Blot are going to do -- I would hope that they allow a person to purchase one license for both Windows and Linux.
In the case of the Mac version, I would bet good money that Windows and Linux keys won't work. Ambrosia is generally fairly active in porting software. Even if Alec and Derek do all of the work on the actual port, ASW will spend a significant amount of time and money on marketing, and they will probably also help with the beta process. I would also be willing to bet that ASW are working with and advising Alec and Derek even now. The Mac version will probably cost a few bucks more, and will almost certainly not support Winows or Linux keys. Whether or not the Windows and Linux versions support each other's keys (or Mac keys, for that matter) is up to Bit Blot, but the Mac version supporting the keys for the Windows version is a discussion between ASW and Bit-Blot.
Also, blue is my favorite color, but you are a very close second, Toom. <3 <3 <3
xander