While the http-options module situation is interesting (and might be a fault – I don’t know that code enough), I think it only affects HTTPS, which isn’t in use here (or do you believe otherwise?). As for the SMTP transcript that was omitted, can I assume that action stopped after the STARTTLS, i.e. you didn’t get later error codes?
Email sends sometimes has advice about error codes (if yours got that far) and SSL/TLS debug (if it did not).
No mail report from scheduled jobs even though it works from send-mail/backup through web command line! has information about the email library that Duplicati uses, showing smtp equivalent to https -accept-any-ssl-certificate and explaining how this is not the same code either. Loosening certificate checking for SMTP does not appear possible short of avoiding SSL/TLS, however because you’re security-conscious and want TLS in use, note that proper certificate checking is also essential to avoiding things like man-in-the-middle intercept.
Maybe you can send Internet Explorer to https://mail-internal.prague.wood.cz:25 then check error messages.
How did you run this test without already upgrading, or are there different systems (if so, how do they differ)?
EDIT: Although I still think the secure way to do this is to debug the invalid certificate (rather than suppress it), testing on 2.0.3.3 shows that --accept-any-ssl-certificate did seem to convert the send-mail results away from an AuthenticationException complaining about the certificate (and you have to add --log-level=Error for some reason to see the message) into a timeout (not totally surprising because I wasn’t going to a real email server but to smtps://expired.badssl.com:443 because I know it will feed me an expired certificate that I can test with). Part of the current problem is that --accept-any-ssl-certificate is in the Advanced options dropdown section of “Configure http requests” although arguably such a concept is broadly applicable to any SSL/TLS connection and this raises a lot of implementation questions about different ways to set things, and scope of the settings. This level of design question doesn’t arise much in this user forum. Unfortunately GitHub issues didn’t raise it.