One of the other things to consider, and probably why BW says it's a problem. There are a bunch of Flashpoints where you have to talk to Satele Shan (republic side) after you complete the Flashpoint. This would likely have to be removed or modified if you didn't return to the Flashpoint entrance. Just thinking this may explain it for now.
Yeah, I was wondering if this was the system that prevented it. Empire side has the same thing where you talk to Malgus at the end. Solution to this might be to put everyone in the conversation when you zone out of the flashpoint, and then just deposit you back your jump off point after the conversation ends.