I think there is something to the thing E. Merckx was saying about JV pulling too hard on some of the last stages. That will have used some energy Roglič might have been able to better use for the TT.
But the big thing is if they hadn't pushed as hard on those stages, would they have still kept Roglič in yellow. It's interesting, but I'm iffy. I didn't think of that during the TdF and so I don't know what and where others were. Particularly Pogačar, he might have been saving more energy than others at key times.
Quintana had a habit of always being right on Froome's wheel in most any TdF. If Quintana was a decent TT person, he might have pulled out a win on the 2013 TdF. If he matched Froome's times on the stage 11 and 17 individual TT's, then Froome would have had to make up 7 seconds on him in the remaining 3 stages. 4 if you count stage 21. Not impossible, but would have made a more interesting fight to the finish.
And the things that make Quintana not such a great TT person, might have added to the bad times he got for some stages he finished well behind Froome on but did make the podium with Froome for the overall. Don't know on that though, I've not got the memory or stats to defend any of that.