I just installed the Thules on my Westy. Eight little holes is all it took. The artificial rain gutter kit comes with a big rubber gasked so leaking shouldn't be a problem. I put the top up and then down several times and I don't see any problem as far as the canvas is concerned. I'm partial to Thules as I've had them on several different vehicles, and these seem pretty sturdy. I stack up to six surfboards at a time on them and travel several hundred miles. 
My .02 worth.

Leo Lipert
San Juan Capistrano, CA
'84 Wolfsburg Westy with leaky heads
'00 Golf