FileMaker 15 Server installed without issue on Mac OS X Server 10.12.5 and works fine as long as you redirect the http/https ports when you install FMS. This has been working fine for a year. No issues whatsoever.
FileMaker *16* Server now complains about Apache running and the only solution provided by FM Tech Support is to uninstall Server.app and reinstall it after the installation of FMS 16. This is a *terrible* suggestion because uninstalling Server.app disables the Firewall settings I have configured with Server.app and opens my Server to the internet -- just to install FileMaker 16 (and presumably every single update thereafter.)
I can give you many reasons why we use Server.app along side FMS server (not least of which is the ability to control database access with the users/groups created by Server.app).
With the FMS installer now giving you the option to redirect the web ports, there's really no reason for FMS 16 to *not* install correctly (like 15 does) on an OS X Server.
Please release an FMS 16 installer that works properly with OSX Server.