Same problem here. I really like the Smart Battery Case, but disappointed Apple couldn't figure out a way to build-in a 3.5mm headphone jack somehow. My Bose QC20i in-ear noise-cancelling headphones are my absolute favorites for travel, gym, and even critical listening - they are very pleasant for most music. However, the 90-degree plug on them is just every too short to fully seat in the iPhone through the Smart Battery Case. I even tried shaving down the excess thickness of the over-molded plug on the QC20i's and while I had some success, it isn't anything I'd recommend.
Now I am looking for a decent "TRRS" style jack extension. I tried a 90-degree, but it proved too thick. Too bad Bose didn't build in Bluetooth to that battery dongle! For now, that is my solution at the gym, a cheap Bluetooth MPOW receiver, but that gives up control/mic functionality.
Maybe someday we'll see a Lightning plug version of the QC20i's with no battery pack. Wouldn't that be great.