are manufacturers required to punish RTOW further by flexing the speeds also?
Short answer is no. The speeds largely come out as a result of the available (presumed) thrust and weight. As a very general observation, and presuming we are above the Vmc limiting weight range, V2 will relate to weight (stall speed), VR will relate to thrust and weight and is calculated to result in achieving V2 at screen height, while V1 will depend on the relationship between thrust, drag, ambients (including assumed temperature) and runway distances.
I wouldn't sweat it too much. The protocols require a degree of conservatism ... if you want to have a bit more up your sleeve then don't flex quite so much but that, really, is not necessary routinely.