Thanks for your patience as we reviewed this functionality! Our SmarterMail team looked into this and believe that this is working as expected.
There is not actually an autodiscover.xml file that is created by SmarterMail. This can be confusing because the link does say to go to http://mail.smartertools.com/autodiscover/autodiscover.xml.
However, this isn't a file but rather an HTTP handler on SmarterMail to listen for these requests. In our initial testing, we were seeing odd behavior as well. However, this was actually due to SSL being disabled while the SRV records are configured to point to HTTPS. Once we enabled SSL, autodiscover worked as expected in our testing environment.
I hope this helps! Let me know if you have any other questions or concerns, or if you're still having trouble getting this to work properly.