Re-reading it, he did limit his rule to not using HTML for _connectors_. I can't refute that; that sounds like a bad idea for anything that isn't a toy POC (which this submission certainly is).
I do think a mix of HTML (for boxes) and canvas/svg (for connectors) is viable, however.
If you can mark up where the connectors go in a way that makes them accessible, you have some chance of making this work.
I think it would require extensions to HTML. There are already mechanisms for linking some elements to others, but most of them have pre-defined semantics (labels for controls, headers for sections and widgets). The closest is probably the `form` attribute that links form controls to a non-nesting `<form >` "parent" element... but forms are a worse hack for a flow chart than CSS connectors.
I do think a mix of HTML (for boxes) and canvas/svg (for connectors) is viable, however.