Becca,
I have a new Felt with the same setup. My guess is that the Tiagra level shifters you have are only available with a triple front shifter. This gives you an extra click ,as you said ,to use it with a double front crank. Yes, it's something you don't really need, but Shimano STI shifters usually have a "preload" shift in the front derailleur to help move the chain up or down. In my experience, it's not worth trying to eliminate this extra partial shift. It can be done, but you'll likely run into more chain/derailleur alignment issues in the process. On the upside, if you ever decide you want the extra low gears possible with a triple, you'll only have to change the front derailleur, bottom bracket and cranks and not the shifter. (I know the compact double is supposed to have the same range as a standard triple, but you can go lower with touring gearing.)
Did the compact double affect your decision to buy this bike? Or did you love it for other reasons and didn't mind the double? I have a Jamis also and looked at the Ventura Race.