Here is my take on the subject. I am about to put a vinyl roof on a car that didn't have one and here it what I am going to do. (just note, I haven't done this yet, but it makes sense to me) I think the key to fitting is the location of trim is the location of the clips.
On a vinyl top car the clips mount on top of the vinyl, which also raises the clip up the thickness of the vinyl (the clips bottom out in the window "well"). So I think the key is to drill new holes for the clips when changing for vinyl to non-vinyl or the other way around.
Again this is just my theory which I will be testing in the next few weeks.....