I never heard of this rule before.
If the punctures are very close to each other, its possible the inside patch method would not work, because the patches would overlap. But if they are more than 2 inches apart, you should be fine.
It's possible this may be a policy to prevent an attempted repair of a tire that is too badly damaged. But it probably is too conservative for most situations.... or Pep Boys may have been trying to sell you a new tire.
