If the stock 261 pistons sit significantly lower in the cylinder than the stock 235, my guess would be that it was done to compensate for the larger volume of the cylinder of the 261.
If the goal of GM was to maintain a compression ratio similar to the 235, lowering the dome height of the 261 piston would be one of the easiest/least expensive ways to do it.
GM wasn't trying to make race engines back then. They were trying to make them run well on the gasoline available at the time.
Carl
