lockup is what they are talking about, it's the last piece of hardware sandwiched between an automatic transmission and the output end. It will lock the output to the transmission when it can to save gas, when you accelerate out of a steady speed (over 31mph) it will unlock, it will also unlock as you decelerate.
That was one thing I mentioned too as a possibility but the only part that doesn't make sense is the speed you're noticing things happening is under where the torque converter would lock up.
That it vibrated for you in any gear is a sign that should lead us to believe that the problem isn't in the main guts of the transmission, like the gears or the clutches or the valve bodies.
So did the dealer agree with you that something was felt, but that there were no codes thrown, thus it's "normal?"
The railcar thing sounds like total BS, Honda ships 80% of its vehicles made in the US via rail. . .it would be an epidemic if they were doing something wrong. And a lot more CRVs than Crosstours come out of the East Liberty plant and get loaded onto railcars, there should be like 10 CRVs for every CT that has a 25mph shudder if this is the culprit.
I heard they totally baby them when they load them in those railcars!
In all honesty I heard Honda does have some pretty cool railcars.
Long story short - if the dealer agrees that your car is having a vibration, then ask to take a test drive in another crosstour on the lot and show how it can't be duplicated. Then ask for a loaner and tell them to call you when yours is fixed. Start documenting this very well because 3 visits and they can't fix this and you might be able to lemon law it, in my state you could if that were the case.