Here is a list of situations in which we use the main domain concept:
myhostnamein postfix config, used as EHLO and reverseDNS (refering to https://mxtoolbox.com/emailhealth test it should be a FQDN, so a subdomain)
Finally we can imagine some apps use the main domain too, see https://github.com/search?q=org%3AYunoHost-Apps+main_domain&type=code https://github.com/search?q=org%3AYunoHost-Apps+current_host&type=code
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