All subheadings begin with subsection numbers

I might be wrong, but I assume those dots are part of making a bulleted list. Of course without seeing the underlying XML I can't be sure.

If you go to the subsection itself, its title still includes the '. '. it looks fine when you have a list of subsections (just looks like a bullet-list), but when you're just looking at the subsection, I agree that it's ugly.

Moving to yelp package - these tables of contents are automatically generated.

What would you suggest? Those are items with bullet points which is a classic presentation

I suggest nothing extra at all. Standard presentation for subheadings is to use a smaller font than the main headings, and Yelp already does this. (Actually, since the headings and subheadings are also bold and differently colored, they could both easily use even smaller fonts than they currently do.)

Since I reported the bug, the formatting has been changed so that the subheadings are numbered: for example "7.1. Install/uninstall .deb files", "7.2 Convert .rpm files to .deb files", "7.3. Install tarballs", and "7.4. Install .run packages". Numbering makes sense for paper books, which are often read sequentially, and have a single nested table of contents and cross-references to numbered sections instead of hyperlinks. Numbering does not make sense for help pages, which use hyperlinks instead and are designed around random access. And it especially doesn't make sense to have sections numbered "7.1", "7.2", etc when there is, correctly, no section numbered "7". Please remove the subheading numbering.