I have yet to see this anywhere so here it is. My top was rubbing until I went to Mecca when the fine people at the Wilmington Boxwood Plant fixed it for me. In fact he fixed it so quickly by the time I turned around from talking to one of the quality engineers about my seat they were done.
I asked the gentleman if he could show me what he had done so I could share it with others here. The following is what he did to fix the rubbing.
First of all, everyone knows what I mean? On my car that top rubbed the side door glass on the passenger side as indicated in the following picture.
[attachment=1]
It is necessary to put the top down to make this adjustment. There is one for each side of the car depending on what side the top rubs. Here is a picture showing the location of the stops from the rear of the car with the top down.
There is a small pal nut on the back of the adjustment holding a strap that we are going to loosen so in order to turn this stop. You will have to loosen the pal nut a bit. Insert a small screwdriver underneath the sheet metal nut and pry it back a bit.
After loosening the pal nut we have to measure the distance that the stop is from it's mounting point. Mine was about 17 mm.
I was told that a 1mm adjustment of the stop will give you about 3mm of additional clearance between the door glass and the top. Loosen the lock nut for the stop with a 10mm open end wrench.
Raise or extend the stop towards the rear of the car for clearance. After you are done simply tighten the lock nut again, raise the top and check for clearance.
Gotta be one of the easiest adjustments to make on the car and beats the heck out of waiting for a new top after you have worn a hole in your old top. Thanks to the fine people at the Boxwood plant for their help fixing this.
Went to the Saturn dealer today, (now called Serra Chevrolet) since last week to have them check out the left and right side seams on the convertible top where the curvature/corners of the windows rubbed and worn almost through but not too bad and I can live with it... but on a good note the 'new' ex Saturn now Chevy dealer retained all their Saturn techs that are well trained on the Skys.
When the service manager came to let me know they were done looking at the top where the seams were worn ( about 1½" of the seam on each side in about the same area in your first photo (circle), then he told me that the tech adjusted the trim adjuster bolts. and it will not rub anymore, ( and I thought that was it..job complete)
then he says, that way after they install the new top it will not get the glass rub anymore and to bring the car back for the install when the new top comes in !!
new top ordered... (3/36 warranty work too!) YAY !
he said it'll be about a 4 hr. job and I will have Reputa (the Beauta) back the same day.

(ie:retained all their Saturn techs that are well experienced with the Skys)
I read on the 'other' forums some have waited days up to a week for new top installs