Update with the OSX 5.0.4 server version...
I took the plunge and did a remote update on my server from Yosemite to El Capitan, my server is some 4000 miles away with little chance of a quick and easy re-boot if it went wrong... but...
1. After the update - which went perfectly, with the correct DNS settings being put in by the update, which is a big fix from Apple, all is going well.
2. Even though I did the Wiki fix (in this post) before the update to El Capitan, I noticed this was over written, so I applied again - again - all is now fine.
3. I note that server app 5.0.4 under El Capitan works very well, much, much faster (mail just fly's alaong like never before, as do most of the other services - excellent news). To be honest, it looks like server app 5.0.4 is written and tuned for for El Capitan - even though is it supposed to work on all OS versions...
4. After the update to El Capitan, DNS settings are all returned to normal - someone is listening to our needs :-)
My advice, do a backup - upgrade to server app 5.0.4, run this to do the data upgrade, then upgrade OS to El Capitan, then run server app again (it does another update), then do the wiki fix...
All I need do now is to work out how the iOS share works under file sharing/share points, and my smile will return...
Dan