The reason for this issue is that the paragraphs in all our Canonical websites have a width limit to help with readability. When lines of text become too long it makes them harder to read, so we limit this width to improve legibility. When you add custom HTML to centre align the elements on the page, what happens is that the container of the titles has a different width as the containers of the paragraph, which makes your page look misaligned.
As for your question on markdown, we support CommonMark without any extensions in Charmhub.
Most developers don’t customise their readme much, so we have chosen to be consistent in styling across our charm detail pages. I would suggest as little custom styling as possible should give you the best results.