I would not worry about it. Especially if the recruiter is willing to affirm that they told him to put it on his record.
What they might separate people for is being actually allergic to something common like penicillin and then not telling them in order to enlist (that is a disqualifying allergy). Saying he is allergic because he is sensitive to something and wants to be cautious is somewhat different.
Get in touch with the recruiter and let them know is my advice.
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