FileMaker Server 13 was the last supported version for Mac OS X Server. For a listing of supported environments for FileMaker Server, see Knowledge Base Article #5677 at:
I recommend posting this to the Product Ideas board at: Product Ideas
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This is a very unfortunate change. FMS 15 worked just fine with OSX Server. FMS 16 is a security step backward because of this installation problem.
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Have you tried the suggestion by electon in this thread:
Edit this file: /Library/Server/Web/Config/Proxy/apache_serviceproxy.conf
Comment or remove the following lines:
I've tried it with FMS15 and Mac OS Server on both El Capitan and Sierra, and it works just fine!
I have not tried this because FMS15 installs without any modifications on OSX Server. I'm fairly sure, the FMS16 installer is looking for any instances of httpd running to throw up that alert and not the ports use (even when no ports are actually being used...)