I've never heard of a county license requirement for an ATM and assume it's just an attempt to raise revenue, not to actually regulate. If it was a more serious requirement, such as one that would require registration with the state's department of financial institutions, I would say you need to mention it to the customer, but report it to the state.
Here, I'm just not so certain. If it's the ISO's compliance requirement, you're not banking the ISO. If it's your customer's compliance requirement I would probably draw it to their attention, then drop it. I'm knowingly leaving myself at the mercy of the examiner who cannot find anything else, but just refuse to stoop to the level of enforcing county ordinances. Besides, I would really like to hear exact wording of the examiner's criticism...
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In this world you must be oh so smart or oh so pleasant. Well, for years I was smart. I recommend pleasant.