using Debian 10 buster - but should not matter.
When you create a Website redirect, ".well-known" is correctly excluded in the RedirectMatch.
RedirectMatch ^/(?!.well-known)(.*)$ https://new-domain.tld
But then, mail autoconfig does not work anymore, so I'd suggest to do something like this:
RedirectMatch ^/(?!.well-known|mail/config-v1.1.xml|cgi-bin/autoconfig.cgi|AutoDiscover)(.*)$ https://new-domain.tld
or may be include all such ScriptAliases, if any?