I have seen this problem before in my shop. We often can use a long air nozzle and blow out the drains and debris from the area in the well where the conv. top mechanism sits. This is where debris gets in and cloggs the drain so water would then fill up and enter the vehicle. If they can't find the leak that is what I would have them check first. Does this area drain correctly? The drains are under the linkage where the rear parcel shelf lifts up. Often with a light you can see the water pooling in this area.
I did actually have one that was just too full of debris and we did need to remove the top to clean out this area well. But in most cases the can be made clear with a long nozzled air gun with shop air. If the top does need to be removed to clean this one then I would recommend the dealer do it. I would ask the dealer to try blowing out the lines first and offer to pay a smaller fee to try to clear them out to save some money. Hopefully they will be able to perform the repair this way. The down side is that you can never get all of the stuff out that is there and it could happen again. As a suggestion try to avoid areas with a lot of leaves or needles or small particles that could work their way into the drains.
I hope this information is helpful. Please accept and thank you.