I just received mine.
I'm happy to report that with some headphones with L-shaped 3.5mm jacks (I have Sennheiser IE8s), the case can be used in the more stable of the "upright" configurations - the one that doesn't rely on balancing the bottom edge of the tablet on the small ridge on the front of the case (which I wouldn't imagine would stay put if used on a train or plane table).
There is a tiny
amount of clearance between the headphone jack and the desk, though I think that as the material of the case flexes over time and the hinges become less rigid, the headphones might end up touching the desk. Probably not enough to ever cause concern though.
Overall I'm happy with the case. I'll probably continue to use the tablet without it at home, as it's considerably heavier with it on, and less comfortable for prolonged graphic novel reading sessions. For travel however, it's much more convenient than my previous solution, which was a separate stand (AmazonBasics - http://www.amazon.co.uk/AmazonBasics.../dp/B006ZT4VA0
) and a £1 neoprene case.
The Amazon stand is excellent by the way, I just prefer to carry as few things as possible.