As much as it could be an inconvenience for a pilot some times, auto shutdown was a part of BT since early tabletop games, where overriding shutdown in time required a pilot skill check. Main purpose for auto shutdown is to prevent mech reactor explosion, caused by overheat, in case of pilot being unable to handle the situation, i.e. when he is dead, unconscious or otherwise incapacitated. Keep in mind, that passing out from reactor excessive heat isn't that rare for mech pilots. At that time, it would be too late for manual shutdown.
Gameplay-wise, it's just another thing to keep in mind when piloting heat-intensive assets. Just think, if auto shutdown would be turned off, instead of shutting down, when you were too slow to press "o", your mech could explode or become heavily damaged because you were too slow to press "p".