I don't believe the data indicates a higher thrust for the second aircraft.
Firstly, Vr is not just chosen as any speed below V2 and above V1. Vr and V2 are a matched pair - rotation at Vr should see you at V2 at 35ft (adjust per rules and runway conditions). You can't move Vr relative V2 without good reason.
Now, the Vr-v2 "spread" is much smaller in the second set of data - almost zero at the MTOW case. Which leads me to suspect that the thrust in the second case is significantly lower.
The V1 being driven by V1mcg seems highly unlikely - I'd expect to see a near-constant V1 at the minV1=v1mcg for a range of weights. The fact that V1 varies considerably with weight implies that there isn't a v1mcg effect here. I think the braking system being different and rebalancing between ASDA and TODA is far more likely.