yes that is how they get installed. I called the company and they confirmed. Not really needed with the hard top installed but suggested with it off to avoid someone pulling a wing upward to access the area. Also, they provide two different length screws and you could have used the shorter ones so they are flush. The longer ones are for when the soft top is installed and these plates sandwich the soft top plastic trim piece.
Here’s how I installed this wing pieces. Not sure if it’s correct. I have a 4dr Sahara hardtop.