I would trim it so it ends under the cap
Stop the vinyl under the trim cap. What's the point of the cap if you run the vinyl past it?
The line workers probably only had a few minutes per car to install a top. I'm sure some came with the vinyl trimmed long. The "intent" of those caps is to end the vinyl there. Unless you can prove your car originally came with the vinyl trimmed long, finish it under the cap.
On a side note, make sure you remove those pieces before having the body blasted. I had one where the screw stripped and didn't want to come out. I decided to just deal with it later.
It was a PITA trying to sand and polish that piece once it had been blasted.