Aha! Ok it took a couple tries, but it worked.
- Change your email address to the one you want to use with your custom domain.
- Under advanced settings, specify your login email address in both IMAP and SMTP settings.
- Also set your IMAP and SMTP servers! Otherwise it’ll try to use servers at your custom domain. For Fastmail, that’s imap.fastmail.com and smtp.fastmail.com.
Not very straightforward, but if you’re using a custom domain, you’re probably technical enough to figure it out.