I didn't realize that had been a problem, but makes sense. Imagine the complaints when a person watches a movie in landscape mode (is there any other way?), and the left and right audio both come out of the left side of the phone? A rocket flies of fun O the right side of the screen,and all the sound comes from the left side? Get ready for a new thread!
There were also some CAD renderings of the inside of the case showing those left indents not going all the way through -- so purely decorative. On the other hand, Aple might have some other purpose for them.
If there is a second speaker, it might go into stereo mode when the phone is held in portrait mode, and mono in landscape (or doing mono phone calls for added volume, etc.). But it would be ridiculous to get rid of the headphone jack for this purpose.
I'm hoping that it's some kind of inductive charging port, or other signal pass through.
Why would headphones come standard with Lightning plugs when not everyone will use them with Apple products? Headphones will be platform agnostic, and customers will buy whatever connection cable that best suits heir needs. And why do you assume nobody at Apple ever had the same thought that in doing this there would be no way to easily charge the iPhone while using headphones at the same time?
Why would that be an issue? There will likely be simple, unobtrusive, inexpensive, adapters to connect any set of headphones.