Yes. It's an issue with DPI - that much I'm sure of. I was able to duplicate the problem on my non-Retina display by changing the clipboard image's DPI to 144 after I did the Copy as Image.
So my fix (what I hope is a fix) is to force the DPI to 72 then mess with the image, then change it back to whatever it was originally (144 for Retina displays).
If you were to use KMFAM Add Action on the Retina display to add a new favorite action, then use KMFAM Select Action and highlight the newly-added action, you should see the issue.