I think the reasoning is that in BW, the champion isn't able to be battled until the postgame, whereas with all the other games (including Emerald), they are fought on the first round of the E4. Also, it is very hard to train your team after beating the E4 in Emerald, with no real postgame trainers to speak of.
I think the idea is that once you defeat the Champion in your game, the challenge is completed. Obviously, GSC/HGSS is the exception, but Red has been the acceptable end to those games for years, especially when you consider how short the games would be without going to Kanto, and the fact that there are more gym leaders to defeat as well.
I also want to stress the fact that the Monotype Challenge isn't an original challenge, and the main rules governing it, especially where the finish line is, have become standard for it, especially since it's been around for so long. If you make people finish at Steven for Emerald and the Cynthia rematch in Platinum, people like me who have completed the challenge before would not qualify. So I think continuity is very important (as is an active thread owner, of course! :D).
