I have found Anchor not found by zola, but it works in browser, post-hoc, so obviously this is expected behaviour.
So, I am clearly not using skip_anchor_prefixes correctly. My current config.toml has
[link_checker]
# Skip anchor checking for external URLs that start with these prefixes
skip_anchor_prefixes = [
"section",
]
In the hope that this will match “section-two” above. But the link checker is still reporting an error.