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Actually, sys.prefix is '/usr' because '/usr/bin' is in PATH while '/bin' is not in PATH. After adding '/bin' to the start of PATH, then sys.prefix becomes '/.' when Python is run as 'python3'. The confusion comes from the '/bin' symlink (archlinux is not a perfect choice for those tests). Whatever the value of PATH, '/bin/python3' has also '/.' as its sys.prefix.
So Modules/getpath.c fails to get '/' as the prefix in step 3 of the algorithm described at the top of the source code and uses '/.' (i.e. PREFIX) instead. This is caused by its reduce() function not handling the corner case where Python is installed on '/'. I will update the PR shortly.