In each civ version tile output is changed. That's nothing more than this, IMHO. Idon't see the problem.
The problem is that a hill is +1H, while stone (which is a bonus resource) is also +1H. What's the point in having bonus resources that basically turns your flatland into hills yield-wise? I can understand that resources on ice/tundra etc won't have great yield, but there is no logic to grassland plain with stone = vanilla grassland hill in basic output. If this is the case, then why have +1H bonus resources at all?