For DNS challenges, I personally prefer using acme-dns. It’s a separate DNS server that only serves ACME DNS challenges. I felt a bit uneasy using an access token for my actual DNS host since it grants full read/write access to every record.

Let’s Encrypt follows CNAMEs and supports IPv6-only DNS servers, so you could just run acme-dns on a spare IPv6 address (assuming your internet provider has a static IPv6 range, or you have a VPS with IPv6).