Thank you very much for all the comments, Simon Krughoff. Here are my responses – I will of course fix the typo's, etc.
1. I agree with the issue of the relative flux calibration issue, and how it makes some of the figures relatively uninformative. Unfortunately, I didn't notice this until I started running lots of examples using this particular CCD. However, that being said, I have seen it in other DECam images and it might be an issue with either the flux calibration or background subtraction (although I don't think that background subtraction should cause this problem). I will make that clearer in the document. Also I will point out that on simulated data this is not an issue so maybe it points to a problem with the normalization and/or over-sensitivity of Zogy to errors in the normalization.
2. Yes I can make tickets on all the issues and add those to the document. Who to assign them to?
3. I can make a minimal data repo with these same example data.
4. I will search for a DECam example where the flux calibration issue is not evident for Zogy.