This might confuse things a bit, but I don't believe the sunroof is supposed to be perfectly flush with the rest of the roof. On my car at least, the front of the sunroof is perhaps 1/16" below the roof, my guess is that this is deliberately done to reduce the potential for wind noise. To my knowledge, my sunroof does not leak.
The link that you provided looked like a pretty good write up, but if your sunroof otherwise works fine, then my hunch would be the seals need replacing, and again that link seems to provide the step-by-step procedure to do the job, just different parts.