Web Server Settings in FileMaker Server 12

I integrated a credit care payment gateway (by Nelix Transax) into my database solution about two years ago.  What I was not aware of at the time was the fact that the gateway provider requires my server to be scanned on a quarterly basis by ControlScan (even though I do not record or maintain any credit card information in my database).  My solution also includes SeedCode's Zulu software creating an iCal server (using port 80).

My most recent scan failed as a result of two vulnerabilities:  the web server autoindex is enabled and the Apache ETag header discloses inode numbers.  In my web server deployment, I have turned off PHP and Instant Web Publishing but I have to use XML (for Zulu).  Since FileMaker is using it's own copy of Apache, I can't find how to correct the two vulnerabilities causing my scans to fail.  I would certainly appreciate any guidance or insights that anyone might have.

(I am hosting my database solution via FileMaker Server Advanced 12.0.5.551 [although the About window STILL says 12.0.3.327] on OSX 10.8.5.  I have not upgraded my server machine to Mavericks due to the issue with FM Server 12 and Mavericks preventing the server from sending e-mails.)