Interesting thread.
Don't think I can answer the question but another difference between the 2 is that they only have 5 engines per season to inculde Friday practices but the gear boxes that have to last 6 races don't need to be used on the Friday. (I have no idea why though).
Also I guess engine performance differs on the age of the engine (a fresh engine being more powerful than one towards the end of its life) and some tracks are more reliant on power than others so the teams swop them around depending on track characteristics and age of parts. In my extremely limited understanding of mechanical things I would have thought the performance of a gear-box would not change? it either works or it doesn't (although as it nears the end of its life I guess its more likely to go wrong)
One thing I don't understand about the gearbox rule is that if a driver has to change a gear-box before the 6 races are up and so takes a penalty and then puts in a brand new gear-box, why does that gearbox not have to last 6 races? (they are then able to change it again at the next race)