What do you think of placing that empty lit.cfg directly within Inputs instead? I think this would generally isolate all Inputs/* test suites from lit/tests/lit.site.cfg and thus avoid such confusion for future tests.
Of course, we might not create any new tests for nonexistent directories, but we might do something else. For example, if we were to forget to create a lit.cfg in some new Inputs subdirectory and it inadvertently came to depend on some configuration item from lit/tests/lit.site.cfg as a result, the new tests might pass locally but then fail under Windows in the manner we just saw. However, if it couldn't pick up lit/tests/lit.site.cfg, then hopefully we'd notice the missing configuration item on any platform.