The actual heat and pressure sensing inside a cylinder is a very difficult thing to do. All sorts of things can lead to problems and having a high temp inlet charge is one of them.
Just because an engine seems to be producing less power, doesn't necessarily mean that it's running cooler. It could just be less efficient and running hotter in certain areas, again a very difficult thing to measure without very high tech equipment, a dyno and then a rip down to see what has been occuring.
This was exactly the sort of thing we used to do at uni with car and bike engines of different designs and there were very often results that were unexpected if you looked at the engine in the simplistic way that most pilots would. There were certianly a few that didn't fit the model I had predicted.