To me, what's making his ground strokes weird in the 1st video is that he never uses his left hand to support the racket either on the handle or on the throat in his ready/neutral position. Only time he has both hands already on the racket is when he is getting ready to return a serve.
Biggest difference between his ground strokes in the 1st and the 2nd video isn't his straight take back or his take back being loopier, but the fact that now he puts his left hand on the racket for support after hitting a ground stroke, both after a FH and a BH.
His take back being loopier in the 2nd video could be a result of both his hands are now supporting the racket which is naturally creating a more acute angle in the way he is holding the racket (by the throat) in the ready/neutral position. Still doesn't look all that natural to me. Especially for me considering when I used to hit with a 2HBH, my left hand was on the handle (I'm a righty). My left hand would slide towards the throat of the racket as I made my turn to hit a FH. He has his left hand on the throat and slides it down to get ready to hit a 2HBH. I think Nadal does this as well so it might not be uncommon.
Thanks for the videos. Very interesting.