Instead of creating the initial 32-bit HDR merged photo in Photomatix Pro, create it in Photoshop CS4 and then save it as an .hdr file. Then do the tonemapping portion in Photomatix.
I wondered why he recommended this because I really couldn't find a justification as to why. But, I think one of the reasons was because Adobe's alignment "engine" (for lack of a better term) is much better than Photomatix's. For an example, I'll use a part of my Williamson County Courthouse and Tree shot that you can see on Flickr:
Shot 1 above is the shot after it was created in Photomatix and shot 2 below is the one created in Photoshop. Check out the difference in alignment! Most of my shots are like that toward the edges and it's been bugging me for quite a while. I just can't get over how much better it is!
However, I noticed that the colors in the shot created by Photoshop are not quite as vibrant, but I think that can be overcome with a little post-processing. Also, there are some artifacts that are dealt with a little differently, but nothing that the normal post-processing won't take care of as well. The only other downside is that it takes quite a bit longer for Photoshop to merge the shots than Photomatix, but the wait may certainly be worth it. Scott Kelby is THE MAN!
I'm certainly happy I got this book and can't wait to try it on some new shots. Now, to find the time and the place to get out and shoot. Hmmm... Where to go...?