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In the subprocess test named test_executable_without_cwd and when the test is run on the installed Python, argv[0] is not the python executable and calculate_path() in Modules/getpath.c, as a last resort, searches the directories pointed to by the preprocessor variables PREFIX and EXEC_PREFIX defined in the Makefile. So this test indeed would have failed with the (rejected) proposition made in issue 1676135 to substitute the prefix '/' for '' in the configure script. But the test would succeed when the substitution replaces '/' with '/./' as proposed here (after Python has effectively been manually installed on '/' of course).
Actually using '/.' instead of '/./' is better since the configure script will remove the trailing slash anyway. In both cases the value of prefix in the sysconfig module is '/.'.