GNU FDL or CC would be the ones to choose since a specification is a
technical document and not code

Typically the license for technical documents like this are either
mentioned in the front matter (check any book; the copyright details
are in the first five pages) or in the footer (check many wikis; they
mention the CC clause at the bottom.)

Depending on how serious things are one might also trademark the spec
name. While the spec itself might be CC-BY-SA which allows anyone to
modify and republish the (attributed) changed version, not having a
trademark means they can just call the modified version the same
thing. Mozilla is one such place that uses this scheme (you can make a
fork, but you cannot call the fork Firefox.)

 - Headings generated by Sourcehut have IDs (good)
 - Links to said IDs are generated as links to commits (bad)

Relative links to content within the same file probably should take
priority over content outside of the markdown file.