Some toughts:
If the 205s prop would be less efficient in transmitting the engine power than the 109 prop, then this would be noticable across the whole perfomance range.
Matter of fact, it would then be slower on MIL than the 109, but it isn't. Also climb and acclereation would suffer, but they doesn't.
Regarding the efficancy of the cooling system, while this may have an influence in real life, AH engine model keeps things a bit more simple. Lets take the example again with the 202/ki-61/109E: Three different aircraft, thus different cooling systems, but the same engine. All three have the same WEP parameters. Or the RR Merlins, no matter in which AC its installed, all get the same WEP. Same with the V-1710 or the R-2800.