Basically, the Miox rep is saying that the Steri-Pen's one great advantage is speed, however the MSR is more flexible in terms of treating less-than-clear water and can reliably treat a wider variety of pathogens.
For me speed is an issue, mainly because chemical treatments leave me feeling vague about how long I need to give it. The Miox thread mentions 5 minutes for some pathogens, 30 for others and 4 hours for others. How long you leave it for seems to depend on how lucky you are feeling today.
I have an "older" Steri-Pen and batteries could be another Steri-Pen advantage (AA vs CR123a). Looks like the new Steri-Pens use CR123a's now, too, so no difference there.
The Steri-Pen comes in several models. I bought the standard one last week, and it still uses 4 AAs. The Adventurer is smaller (and more expensive) and uses CR123s. So Steri-Pen gives you the choice.