Thanks for your reply, but I am still confused.
The pages I was talking about were not under the root, but under their own section projects/. But I guess this doesn’t make a difference.
I am still not sure how to get the “orphaned page” to get anchor links. Setting insert_anchor_links in the page itself doesn’t work.
If I rename website/index.md into _index.md to make it a section, the markdown.md is not an orphan anymore and will get the anchored links (if enabled in website/_index.md, it does not seem to inherit from projects/_index.md)
But I am losing date and updated front matter since it is not a page anymore, but a section. Plus it is not listed as page the /projects section anymore, because well - it isn’t a page.
I don’t understand why insert_anchor_links is not a setting for the page itself? It only affects this page’s generation anyway?