To elaborate a bit on some parts of Emmabee's answer: the reason that your second example sounds a bit off rather than entirely incorrect is because the verb "stand" can imply either a state of being or an action, and in this case the default sense is a state of being. For example, this sounds fine:

If he had stood when the tornado passed over the ditch in which he was lying, it would have killed him.

In this case it's clear that stand implies a change of position. We often clarify this meaning by adding "up": "If he had stood up" and so on.

To elaborate a bit on some parts of Emmabee's answer: the reason that your second example sounds a bit off rather than entirely incorrect is because the verb "stand" can imply either a state of being or an action, and in this case the default sense is a state of being. For example, this sounds fine:

If he had stood when the tornado passed over the ditch in which he was lying, it would have killed him.

In this case it's clear that stand implies a change of position. We often clarify this meaning by adding "up": "If he had stood up" and so on.