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I can reproduce it reliably.
I ran ./configure with --with-pydebug.
I'm not using NFS, and I'm not aware of anything else unusual about my filesystem.
The fact that a timestamp overflows in the failing test is a red herring -- the following also fails, with os.stat raising FileNotFoundError:
 def test_without_timestamp_overflow(self):
 sys.path.insert(0, os.curdir)
 try:
 source = TESTFN + ".py"
 compiled = importlib.util.cache_from_source(source)
 with open(source, 'w') as f:
 pass
 __import__(TESTFN)
 os.stat(compiled)
 finally:
 del sys.path[0]
 remove_files(TESTFN)
I've verified that TESTFN does get imported by writing 'print("hello")' to the source file.