Using the website link works for verification but yes, it would be nice to have an extra link for Mastodon.
Seconding this in particular as someone with a personal website and Mastodon profile. I tried adding a rel=“me” link to the bio section, but it’s re-formatted in the live page so it’s not viable as a workaround. EDIT: Missed that part of OP’s post, but left this in since the same thing happened to me
Could be interesting to allow multiple custom links at the top or something, would probably be easier than adding new options over time.