Dave,
I have done versions 3.5, 4, and now 5 of DxO. I can't tell you when they will support the 1DSIII, but I can comment on some aspects of it.
As for which modules you get: you actually choose from among all the available ones before you download. Currently you need to install their download manager which makes it very easy to select and download. You can, in fact, get modules that you don't currently own equipment for (such as a lens you are anticipating getting). Or you can download new modules whenever they become available. So downloading is easy.
As for the cost to upgrade: Check their website to see if you can find a price to upgrade from 3.5, or email them to ask. It didn't cost me anything to go from 4.5 to 5. For the 1DSIII you will certainly need the top of the line version, called something like "Elite Pro"(?).
Now as to using 5. When I first tried it I was horribly disappointed. It didn't let me keep any of my presets from version 4, and the new interface was completely confusing to me. Of course I tried using it right away without bothering to look at the manual. I had installed it separately from 4.5, so I simply went back to using 4.5 until such time as I could start trying to figure out how 5 operates.
I have recently managed to come to terms with version 5, but I must say that Alain's tutorial is terrific. It clarifies all the essential points that I was confused about. I have read it and printed it out for reference. Some of what he says I have figured out on my own, but he has lots of good tips that I had no idea about.
I hope this helps.
Regards,
Eric