I stumbled at the same problem. For me, the autoconfiguration did not work in Thunderbird, but only for email domains other than the mailserver domain. So if my mailserver domain is example.org and I have another domain second.org registered to send emails over that server, the autoconfiguration would work for mail@example.org, but not for mail@second.org.
In order to solve your problem, you need to know how Thunderbird does the autoconfiguration. When you add a new mailbox to Thunderbird, it tries to get the server configuration via HTTPS from a webserver listening on the domain of the mailbox you want to add to Thunderbird. If you want to add mail@second.org, Thunderbird tries to get https://second.org/.well-known/autoconfig/mail/config-v1.1.xml. This file contains the parameters for protocols, ports and the mailserver Thunderbird should use. You can see all web requests from Thunderbird in the error console of it.
If you are running the nginx-container shipped with mailcow-dockerized as webserver accessible from the internet, it should do that automatically for all registered email domains. If you are not running it or the port 443 is not allowed in your firewall, the autoconfiguration won’t work.
If you are running an additional reverse proxy, you have to set it up according to https://docs.mailcow.email/post_installation/firststeps-rp/#nginx (this is for nginx). However, if you have multiple domains registered on your mailserver, your nginx reverse proxy e. g. needs to serve a single SSL certificate for all domains in order to prevent Thunderbird from giving you an error message regarding SSL certificate domain mismatch trying to get the autoconfiguration. You could also serve the configuration file manually and statically. Please see my own thread https://community.mailcow.email/d/2246-multiple-domains-without-one-tls-certificate-containing-all-domain-names-as-san as this could help you or others having similar problems.
I haven’t looked it up yet, where you can directly manually edit the autoconfiguration settings in mailcow, but I hope my answer should point you in the right direction.
