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Pretty sure they will count as separate inquiries and both will hit your score. Installment loans and revolving credit are coded differently, not to mention the bank will probably pull a different FICO formula for both auto and credit.
My credit union uses 1 report for 90 days regardless of what you are applying for. YMMV however and you would be best giving them a call and just asking, I'm sure they will tell you if it goes off the same pull or a different one.