I would say wait until the TDF to see what Shimano does. They may be dropping a new Dura Ace and maybe even a new Ultegra. If those two groups are 12 speed, then this gen will be worth a lot less. You can choose either and you’ll be significantly better off than now.
If you get new wheels with the 11 speed freehub, they may be incompatible with all new Shimano groupsets. Do you trust Trek to make a replacement freehub for the XXX4?