I'm a little nervous to pull the trigger on running publish, I admit, because I'm not sure if or how you are determining the rendered file path based on the markdown source from which pages are generated. I have a custom permalink scheme I use with my Jekyll-based sites, so unless sequoia is able to parse that, the URL could be wrong and I worry what becomes of the PDS records.
Could the site URLs be written to stdout as well? Or do those not matter somehow? Perhaps linking to some published records via https://pdsls.dev or something would help.
Looking at one of your recent posts https://pdsls.dev/at://did:plc:ia2zdnhjaokf5lazhxrmj6eu/site.standard.document/3me5ywv7ptv2v I do see a path of /now/the-strangers-case which does indeed map to https://stevedylan.dev/now/the-strangers-case.