Dave,
I guess my response is the same as Rob's. The channel seals really well but a horizontal plane could be another thing all together. The silliest little thing like a small notch in the lexan edge could cause it to leak.
I would suggest a experiment with something like Rob's suggestion with the Sikaflex urethane. Other urethanes might work too. The urethanes are what they use to glue in car windshields. We use this stuff all over the place, a couple of different brands including the Sikaflex. The advantage I would see to gluing it flush rather than setting it in a channel is you won't have the lip to hold water. Using the channel you will have a small lake sitting on the glass just asking to find a leak.
Cary