Well, this is an old thread but to the OP, Yes and No. If you have a plastic flange, or anything for that matter, under the seal it will not lie flat. The tape is there to protect the window seal IMHO. As far as the rear window clips, if my memory serves me right, the directions stated to pull the window seal "out of the window jam" to seat the clips correctly. It was hard to get a good grip on it but I pulled the whole seal out to seat the clips. All is good, no worries...great fit and finish... 
