I'll chime in here. I spent a ton of time looking and was going back and forth between used and new.
I just ordered a 2014 with factory rear bunks. The cost depends on what options, but its $5-7K plus the $1144 special order change fee that you pay once for any non standard interior change. I have some other interior changes made at the same time. They typically add an addition "cozy" heat exchanger, so temp should not be an issue. There is also an AC duct in the ceiling.
I don't see why it could not be done after the fact. It might not turn out as nice and the extra cozy might be an issue. If you kept the stacked W/D, then the just the only the dresser would have to be removed and replaced with the narrower/taller ward. If you do like the Crabtree's, the W/D cabinet also has to get replaced as it is shallower.
If you have questions, let me know. I have been going back and forth with AC for 3 months and have pics, drawings, of all 3 versions.