The short stroke isn't why they get hot ... it's the forged piston expanding and creating more friction ...... coupled with the laid down cylinder ..... With forged pistons it's critical that you have the mixture slightly on the richer side of lean in order to keep the denser forged metal cool .... If you run lean and heat the piston up it'll expand and rub hard on the bore .... that's why they need to run more piston to bore clearance than a cast piston .... And no matter what you read ... a forging isn't as dimensionally stable as a casting at high temperatures ..... That's most likely why they need to be rebuilt every 10 hours when raced as Dready says .....
Early XR75's only have a 41.5 mm stroke and CRF150R's only have a 42.7 mm stroke and they don't overheat very easily ..... even when worked off their heads ..... in fact early XR's have stuff all cylinder finning but still don't overheat even when being thrashed all day long ...... that is ...... unless they are fitted with a forged piston in which case you have to watch the engine temp and let the bike cool down regularly .......
A long stroke engine creates far more cylinder friction under normal circumstances purely because the piston has to travel further with each rpm .... so it HAS to go faster and due to the steeper rod angularity there is more piston thrust on the cylinder wall ........ that's precisely why F1 engines run big bore , short stroke , long rod engines ...... if they didn't slow down the piston speed and reduce rod angularity , they would grenade long before they got anywhere NEAR 19,000 rpm ........