No, it is not the only way to do it. It is the easy way for them so they don't separate the cap from the hull. I personally don't believe that this method is justifiable under any condition but I read that some members think that some boat designs lend themselves better to this method than others; however no one shed any light on the details of the design that justify this Frankenstein technique of "fixing" the boat.
Long story short, IMHO, find yourself another shop, these guys are lazy. Or better yet, roll up your sleeves and do it yourself, it is not that hard and we can walk you though it step by step. You will end up with a much better boat for a fraction of the cost.