John,
You are exactly right, the specification incorrectly refers to coverage based upon the Almen strip. This is why the Surface Enhancement Division of SAE revised SAE J443 regarding the Almen strip to be used only for intensity and then the committee created a separate document SAE J2277 for Shot Peening Coverage. This clearly explains the methods to be used to establish coverage on your part.
I expect that AMS-S-13165 will be revised to address this inconsistency. Contact me if you wish to participate in this project.