I heard a sheriff in the state of Florida talk about this very issue a few months ago, responding to a concerned email writer who basically said the same thing you are saying.
Apparently some states handle their NCIS checks exactly as if they were background checks resulting from a traffic stop, so the federal government doesn’t get information to alert them that its anything other than a traffic stop or some other type of check. I can’t provide you any more proof than what this sheriff said. But there was a firearms dealer who spoke after the sheriff who said the same thing.
NICS and NCIS are not the same. FFLs contact NICS (Nat Instant Check Sys) for the sole purpose of getting ATFE advice to either “proceed, hold or do not proceed” with a transfer of a firearm. Has nothing to do with background checks etc. I believe that the ATFE operators who man NICS query NCIS or other databases to provide such advice.