"Different people generate ./configure different ways.  Some insert runstatedir in configure, others don't.  E.g. on 14 April 2017 runstatedir was added to configure, on 9 June it was removed from configure, on 29 June it was added to configure.  It needs to be clarified once forever, whether runstatedir belongs to configure or not and then everybody has to stick to this, in order to avoid useless changes in the version control."

For practical reasons, we decided to include the generated file configure in Git. You are right that not all developers use the same autoconf version, and so that the generated file includes or not the runstatedir change. I don't know how to fix this issue. If you consider that it's a bug and should be fixed, please open a new dedicated issue, since it's unrelated to your fchdir + -Werror bug.