Pandoc appears to silently append an extension to the template name if it feels like it, which means that you can't use a file which doesn't have the "correct" extension as a template:

$ pandoc /dev/null -o /dev/null --template <(echo)
pandoc: /dev/fd/63.markdown: openBinaryFile: does not exist (No such file or directory)

Pandoc version: 2.3.1, reproduced on 2.6 (though then the extension added is html, not markdown)