I have a feeling this has something to do with the stop wordpress from looking like wordpress thing, but is still a problem for anyone "crazy enough" to use the default permalink structure.
Ah I see what's happening the "All static theme assets are rewritten to the website root" can't work if the default permalink structure is selected as this is basically no permalink structure. Ah so.
Fix #409 - Don't use clean URLs with default permalink structure
fixed, thanks for the issue