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.
In this world you must be oh so smart or oh so pleasant. Well, for years I was smart. I recommend pleasant.