I think the answer is yes, you can put too much in and plug up the weep holes and the inside of the rail. When you do get a break in the seal, the water will travel inside the rail and out the weep holes. With that blocked, it's conceivable that water could go over the inside ridge and down the inside of the wall.
Here's a picture from Winnie what it looks like where the black dot is the sealant you're adding:

The complete guide to apply sealant from Winnebago is here:
http://www.winnebagoind.com/resource...%20Sealing.pdf
I sold my 1999 Chieftain to my nephew in '04 and he didn't maintain the roof seal. In '07 he was caught in strong side/head winds in the pass by Palm Springs and lost about 4 ft of the fiberglass roof. The seal outside had to be long gone years before the fiberglass ripped loose, but he never had any water leaks inside.
The factory seal on my '04 Chieftain was really poorly done....very thinly applied. So I had to redo some of it in yr one, and the whole thing in yr 2. I applied it about 1/4 to 3/8 inch deep and it has held up well for about 5 yrs now. I think the channel is about one inch deep, so you would have to try hard to get it all the way down. Maybe if you used the wrong stuff and it was too runny and flowed down to the bottom. But if you use the right stuff it won't flow.
Good luck,
Bill