Karnak: Different cooling systems at work. From memory of past discussions there has been historic documentation of cooldown times, and it has been brought up before. Can't go into specifics as it didn't interest me enough to save any of it, but I remember it happened. It's not arbitrary, from what I recall. The same type of engine in a different plane is going to have different heat dissipation due to oil coolers, liquid coolers, airflow over both, etc. Not to mention just because the engine is Merlin doesn't mean it's creating the same heat. There are different boost levels creating different heat levels in different planes. The P-51 and the Spit1, for example, are significantly different.
Predator, I don't think you have a good grasp on how HTC models it. The official max power (war emergency power) that is listed in manuals and such is used. That is the 5 minute or 10 minute rating that AH has modeled. The "30 min" setting is basically off-WEP in AH because the increased fuel burn shortens flight time to the point you never have to worry about overheating. The cooldown time was not 1 minute. It was 5 or 10 minutes (I can't recall, but think it was 5). You should check up on it if you get the chance. There were some WEP settings that were only allowed for 2-3 minutes but these seem more rare... Such as GM-1 injection or when you had a de-rated engine and it could only pull WEP for so long. Note the 109E has only 5 minutes of WEP, as does the C.202 which uses the same type of engine. That's because they weren't cleared for any longer than that.
It's all based on documented material. If you think it's wrong, provide evidence to HTC and they will take it into consideration. If it warrants it.