I found that I was setting the default mime type for wp_mail_content_type to be text/html which according to the notes on the codex can cause this particular issue.
I’ve removed the code from my functions file, and the registration email looks better, but (and I haven’t seen WordPress’s emails in a long time) still doesn’t look 100% normal… I need to find another self-hosted WordPress site that allows registration to compare, but is the activation email supposed to look like this?
It’s odd to me that there are two links in the email- one with the proper query strings, and another without. Just doesn’t seem that user-friendly- is that correct?
Anyway, if anyone else runs into this same issue- the current solution for me was to entirely remove the custom wp_mail_content_type function that changes the default MIME type for WordPress email to be HTML.
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