It also adds a severe amount of visual clutter between the code. Individual preference I’m sure, but I’d prefer less comments, I think. Or maybe my IDE just needs to collapse comments inside functions automatically.

If this were commonly-used code at the core of a project, I would definitely agree. However, this is the kind of thing that gets stuck into a CI pipeline and not looked at for months or years, and it's written in two languages (GraphViz and very SQLite-specific SQL) that probably most people don't use regularly. I gave it the comments I'll wish it had the next time I come back to it, to figure out how it works.