It seems that OTF output by Glyphs is non-deterministic.
If I use the same source file with the same version of Glyphs, I often get different binary results, which can be shown with TTX. Of course, some differences in the head table are to be expected but I am seeing differences in the CharStrings in the CFF table as well. As far as I have tested, these changes never lead to functionally different fonts but they make life more difficult when examining the differences between two OTFs.
What causes these differences? Is there any purpose, or is it by accident?