In my humble opinion, what they told you is crap. It may be true that a slightly bended phone causes the problem, but it makes me wonder:
how is it possible that the phone was bent in the first 10 to 12 mm at from the bottom? The bottom and top of the phone should be stronger than it is half way the enclosure. So, the chance it was bended is slight to none. Did you see it yourself? Can you confirm it's bent?
Secondly, if you have your phone in a case, as you state, then the following makes me wonder: is it an Apple case? If so, then the case may not be strong enough and should give you the right to a replacement. Then there's the problem of all those people having this problem. Are all those phones bent? At about the same place as yours is? If so, then I would argue that there is a design flaw in the phone that makes it too weak to withstand normal pressure. This means that it's not accidental bending, but a production/design fault, covered by warranty.
I really think that Apple cannot get away with this. There is a serious problem with the headphone jack. It not only makes many third party equipment unusable, but even the Apple earpads have this problem (in my case anyway).
For me, I made an appointment at the genius bar for coming Monday. I'm very curious to see what they will do. I will insist on a replacement (again) and the guarantee that this problem will not reoccur with the new phone. If they do not go for that, I want my money back and will leave Apple for good.
Come on Apple, how can you ruin a great piece of hardware in such a clumsy way? It's an earphone jack we're talking about! It has been an industry standard since the stone ages. No one, not even the cheapest manufacturer has managed to achieve what you did with the iPhone 6!