There is no severe inaccuarcy in your planner. The "severe inaccuarcy" that you see is just because you forgot to set the suspending temperature to 10001.
So far, your planner seem to be right. Removing the top-left heat exchanger do cause the reactor to explode in-game with a pulsed redstone control. I just tested that. The reactor exploded after burning the top two vents and some bottom vents. The explosion was not very powerful, though.
That should not have made a difference, considering that my planner defaults to a suspend temperature of 8400, which the simulation claims it never reached - if the simulation says it only got up to 3000 and in-game testing caused it to explode (by hitting/exceeding 10000), I'd call that a serious discrepancy. However, I realized there's another possibility besides a mistake in my planner: something could have wrong with the redstone pulse control you set up in-game (e.g. misconfiguration, unexpected hiccups). Could you please explain exactly what you did to get an 8 sec on, 1 sec off cycle in-game?