FWIW, I agree with your decision. At one time, scrap dealers were automatically classified as "high risk." While the classification is now more a of judgment call to be made by the bank, a decision to exempt a junk, salvage, or boneyard from currency transaction reporting would be best supported by a sophisticated intra-bank system for monitoring their cash that did not depend on CTR filing.
As for these operations being buyers or sellers of motorized vehicles, aircraft, vessels, etc. I would guess that once the object no longer moves, flies, or floats, the classification no longer applies. (Vehicles, aircraft, & vessels were put on the list 25 years ago because they can cost a lot of money and can readily be converted back into cash after they've been taken out of the country. I don't think that analysis applies to their remnants.)
If I had to make the call I would rely on FinCEN's advice, not that of my regulator. The only answer the regulator could authoritatively offer on the subject would be one they got from FinCEN.
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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.