Hi Brian,
Probably Ken Stone's article was wrote some time ago.
I remember than 2 or three years ago (search this forum) they where problems when trying to use h264 with Encore, so people had to stick with the MPEG-2. things had changed and you shouldn't have problem using H264 with the software that you have mentioned.
H264 is a better option.
rafael
http://www.nagavideo.com