Absolutely. The three round rule is just a conceit, based on the DMG's recommendation to use that as a baseline for building your own monsters. If you could create a simulation tool as Hemlock recommends, it would be far more accurate. If fact, you could even have that tool account for how long...
I've had much more success recently in designing both encounters and monsters by throwing out the CR system entirely and focusing my encounter work on three metrics:
The sum total of the party's hit points versus the average Damage Per Round of the enemy combatants
The average Damage Per Round...