The asciidoctor-pdf command is not performing correctly.
The problem is the implicit header processor extension including in Asciidoctor PDF. I introduced this extension for the Editions application, which assembles NFJS, the Magazine. However, this extension should not be enabled by default because it's changing the behavior of AsciiDoc / Asciidoctor in the general case.
If I disable the extension, then the asciidoctor-pdf command resolves the chapters correctly. I'll fix this for alpha5.