::I think it was decided to use whichever would be most distinct from the national flag.  That means it's the jack for the US Navy and the ensign for the Royal Navy.  I personally agree with you; I don't see the benefit of trying to be distinct from the national flag at the cost of displaying a flag that's less representative of what a ship would actually be flying most of the time. 
 ::A big part of my reason for creating the template is that everyone can agree to use it, and if in the future consensus changes to using ensigns, we can change the template and instantly get ensigns instead of jacks.  I figure if we make it easy to change from jacks to ensigns, it'll be easier to get consensus to do so.