> When include files are copied around they sometimes treated as the same from "#pragma once" POV (if copying process keeps the timestamps) and sometimes as different (if you put them in GIT and pull back).
I've never seen this behavior. Any decent implementation of #pragma once should not flag two files with different contents as identical. Very old compilers were sometimes confused by various links of link, but this issue hasn't cropped up in a very long time.
Please provide a pointer to a bug report or at a set of setps to demonstrate the behavior you describe.