Please reference http://dev.onlyoffice.org/viewtopic.php?f=10&t=6157#p7803
for more information. Seems to be related.
With DNS custom domain name enabled, ONLYOFFICE does not properly build the activation link. It always uses http (instead of https in my case) with the custom domain name.
Removing the custom domain name option sends the email with activation link to whatever domain name or IP that I have typed in the address bar. So, in this case, it will have the https if that is what I am accessing.