Thank you for your post.
Looking through past issues, I don't see anything even remotely similar. To be sure, I just installed FileMaker Server 15.0.1 on Mac OS X 10.11.5 (El Capitan) without any issues. I know this doesn't help you, but wanted you to know what you are experiencing is not normal.
Uninstall FileMaker Server 15 from the machine. Reboot the server (to clear out any possible memory conflicts, log into the server as the administrator, and try installing FileMaker Server 15 again. If you still get the same issue, then there is something specific to your environment causing these folders to appear.
Keep me updated with any progress.
I checked on 8 FileMaker Server 15 installations that we have done so far on El Capitan. Two of the machines also had OS X Server on them but they had the extra folders too.
There were only 2 of the 8 machines that did not have the extra folders. One of them was running OS X 10.11.2 which is the version it was on with FMS 15 was installed and the other had not previously had FileMaker Server 14 installed on it. All of them were upgraded to El Capitan after de-installing FMS 14 and before installing FMS 15.
In each case we did a de-install of FileMaker Server 14 before doing the El Capitan upgrade but we did not delete the /Library/FileMaker Server folder.
I'm guessing that this has something to do with previously having had FileMaker Server 14 on them. None of them would have had higher than FMS 14.0.3, some would have had 14.0.2.