I know this is an old post but this maybe helpful to others down the road.
I have FileMaker on the standards ports and then installed Bitnami's Owncloud (stack). Owncloud installs a second instance of Apache on the alternate 8080 and 8443 ports. No conflicts.
The only problem I have is with the OS X application firewall (OS X's and OS X Server's default firewall); owncloud works when it's off. Seems to be the same issue I have with with running FileMaker on the alternate ports with port 80 and 443 are being used by a OS X Server; haven't tested this with the application firewall turned off.