Not that it was specifically solicited, but I thought I would give you my impression from all the experience I have in Baja (once), so take it with a grain of salt.
Every since I was a kid and I'm not any longer, (in fact I could race in the half-centurion class now) I wanted to experience the thrill of Baja. Life had other plans for me, but in 2009 I finally put a group of friends together to go give it a shot. The end result was one of the best experiences of my life. Now remember, I'm a Baja newb, goon, idiot, or any other derogatory term you would like to use, they are all accurate. Still, I can ride a dirtbike fairly well and have have had some success racing in my own small pond.
OK so with all the prerequisite disclaimers out of the way, here was what I did. Our race bike was an XR650R and the prerunners ran the gambit. I used my KLX450R as that is the bike I ride and race these days. Now while I have a ton of time on the 650, in fact it is my bike, I didn't have a spare XR to prerun on. So the KLX won the coin toss.
What I found was two fold. Riding/Racing Baja is not necessarily over challenging but it was more difficult than I had led myself to believe going into it. Now remember I ride the KLX quite frequently, but when I preran on it I found myself fatiguing quite easily, that could have been suspension or just bad gearing for the speed we were carrying. Regardless, I was nervous come race day that I wasn't going to be able to hold up my end of the race (I kept that to myself of course). The second thing I found on race day was that when I jumped on the XR650 it was like riding my couch (I know what being a couch potato is by the way) through the desert. The bike soaked up the desert and spit it out as far as I was concerned. Now some of the other riders with less XR time had other opinions, but I am only recounting mine. In the end I was glad to have the XR650, it made it to the finish line and looked like it had been through a war. In fact, it had a war with the desert.
I think Cracker1 suggested using an XR and while I don't know him well, he and I had this same debate after the race as to what we each thought about the right bike for the desert and I think I agree with him for the most part. As I look to my next effort in Baja my thought is to refresh the XR650 and use it again. If I do another team event, then I will certainly pay a little closer attention to what the other riders are accustomed to riding.
As I read your post it seems like you have already decided on the race bike so I am not trying to sway you one way or the other, rather I thought I would tell you my experience of riding a 450 and then a 650 in the desert.
By the way, I should probably confess that my friends call me Sasquatch and therefore that could have some bearing on my fondness for the XR650!