Computer programs dictate the fares and there appears to be little logic to us customers.
As JEK demonstrates, if you google your starting and endpoints, you will receive options to book that passage. The problem we find is you are not often offered all of the options. For example, Tradewind has many flights each day and it may be challenging to pick a connection time between flights. We always err on picking a little more time than the ‘legal’ connection times offered. But if you choose the JEK option, your bag will be checked all the way. However, on the return, you enter the U.S. in San Juan, pass through with your baggage and as Andy points out your bag has to go through the agricultural inspection and receive the inspected tag.