Does FileMaker Server 16 prevent use of the system apache in macOS?
I know that it's possible to run both the system instance of Apache in addition to the FileMaker Server instance in version 16, provided they run on different ports, so I guess that's a 'No' to your question.

For a better answer, I suggest you post the question at the community forum where FileMaker support staff also chimes in where appropriate. You can also report this as an issue there and get swift support from them.

https://community.filemaker.com

https://community.filemaker.com/community/discussions/report-an-issue