I've been working on this again, and made some plots of one of the original "problem CCDs" in a notebook. Within the scope of this ticket, for an ap_pipe run with the old template, it appears that bad columns are masked as BAD in both the calexps and diffims as one would expect. So, that may be sufficient to close this ticket, since I can't reproduce the issue.
However, there is some really weird stuff happening with diffim masks with the new templates. I have been hoping that if we can just filter objects and/or sources by whether or not they are in a masked region, we can get rid of most of the spurious sources. In principle this is correct, but I think something is not working correctly in the present diffim mask assignment, because there are huge swaths of INTRP, BAD, CR, REJECTED, INEXACT_PSF, etc. Maybe this is the result of the coadd template inheriting all/most of the flags when it didn't use to? I'm not sure, but I think it's probably out of scope for this ticket.
I'm going to put this in review, and request Eric Bellm take a look at my notebook at /project/mrawls/
DM-13081-Bad-Columns-Take2.ipynb so we can work together to open new mask-related tickets as needed.