Nah I don't believe that. They brought the break back on Monte Bondone.According to Slovenian press there was always plan to attack the pink jersey on final MTT and Rogla was obsessed with that final climb. I guess that fall has changed dynamic in the mountains so JV were riding even more conservative but we will never know. I am almost certain that they did not want to be half of minute behind and put everything on the line for stage 20.
I believe the overall plan was simply to make sure to peak in the 3rd week, so which maybe includes going into it undercooked by a little bit. I'm less inclined to blame bad ITT setup for the stage 1 ITT, I think he just did a bad ITT.
Then having a bad crash you need to recover from doesn't help you very much when you were actually slowly working towards your peak.
I think by Monte Bondone they got optimistic because the injuries from the crash stopped feeling so bad but that didn't equate to having great legs yet.