Most anyone could play with a standard timing chain setup and test the results. Do you really think if it made any difference in frame flex or BB twist, nobody had discovered the "solution" until Paketa publicized their uniquely pinched rear BB & chainstays?
Maybe this problem is more pronounced and specific to Paketa, hence the need to place the timing setup inboard? Your testing (and friends with same) seems to indicate that the twisting problem is more of an issue otherwise.
One other key point, you are comparing the feel of your previous Pakata to the Vr2 with a much beefier 1.5" tapered fork. I am doing the same... our previous Calfee with our new frame and 1.5" tapered fork. I would not be surprised if the diff you are feeling is not mostly due to the huge upgrade in the front end stiffness as Pakata mentioned in regards to the ENVE fork? I do believe this is a key diff btwn the 2 Calfee frames in our case.