Andrew R Stewart 

I would say there's a conflict between whoever chose the Trek's frame size and your current bike fitter. On face value I'd say you are now on the wrong frame size, IF the new fit is actually the better one.

Trek has had a frame replacement program for a number of years. Usually motivated by out of warranty things (like a too small frame??). This is one option.

Finding someone to fabricate a custom seat mast is another option. Who? I have little idea but there are a number of custom carbon builders out there. Maybe one of them can help. For that mater the mast likely doesn't need to be carbon, or have the frustrating Trek seat rail clamp design.

Going to longer crank arms or finding the classic Shimano DID arms/pedals system to drop your feet further is another unlikely option.

You have some pretty well designed bikes. Do they all match fairly close in stack/reach? Have you changed their seat height (and any other fit specs that this new guy has told you to do)? Have you put many miles in differing conditions with the new fit spec? How were these other bikes chosen WRT the fit? Have you changed in your abilities/flexibility/strength/riding style since they were bought?

We see people coming in often enough with bikes that we feel are the wrong size, usually due more to reach and not seat height though. We do the best we can with what they have already paid for and give them our advice for the next bike if they ask. Andy (who really dislikes the brand specific frame/fit designs that are all the rage these days