A couple of posts commented on contamination considerations.
I suggest that the main concern here is the adverse effects of contaminant depth (and SG) on the net accelerating force. As the aircraft staggers down the runway, first the tyres have to displace the contaminant and, second, the contaminant so flung away by the tyres may impact on the aircraft structure. Both considerations result in drag which reduces the net accelerating force. Reduce the engine thrust and, likewise, you are reducing the net accelerating force.
The usual contaminant depth constraints are there to keep the adverse drag effects in check. However, a real world concern relates to the variability of contaminant depth along the runway and the effects of grooving, porosity and so forth. To some extent, data gathered from significant operations on a particular runway can provide some engineering comfort but, overall, reducing thrust eats into the margins built into the certification data. Push your luck too far and perhaps something will eventually not work out all that well.
My concern would lie more with the degree to which flex might push the calculations toward a limiting runway performance rather than concerns with the philosophy.