I just upgraded my development server with FMS 14.0.4 from 10.11.2 to 10.11.3. I just ran the update without uninstalling FMS. The upgrade went smoothly and FMS seems to be working. I've tested it with FMPA 14, FMGo 14, and WebDirect. All are working as expected.
As always recommended, holding off to upgrade to the very latest version of the OS is best for production solutions. But so far it looks like this upgrade is a smooth one in regards to FileMaker server.