I've had Di2 on one of my bikes. You use the same Ultegra 165 mm crank for Di2 and mechanical. The electronic part only refers to the shifters and front and rear derailleurs. The crank, cassette, and chain are exactly the same as the Ultegra mechanical.

It's totally worth it to change the crank to the 165 mm crank since you're shorter. However, 165 mm cranks are usually more expensive since Shimano makes so few of them, which may be why Trek and other bike manufacturers put the more common and cheaper 170 mm cranks on their smallest bikes and probably why your LBS isn't willing to swap the 170 cranks to 165 cranks at no charge. I'd ask your LBS if they're willing to swap the crank out for the difference in cost between the cranks.