If you are using Server 5.0.4, I agree, Apple's claim to the web ports is a little aggressive. If you are not using Profile Manager and you are not concerned about the web services, you can overcome this by disabling the ports in the service proxy config. You have two options here.
If Apple’s web interface is not needed and you are not using Profile Manager, reclaim those ports by editing the following file:
/Library/Server/Web/Config/Proxy/apache_serviceproxy.conf
Comment or remove the following lines:
listen 80
listen 443
To comment, simply add a # in front of each line. Commenting out the lines is a better plan than deleting. At least if you need to revert, you can simply remove the # character. Reboot the server and now your 3rd party tools have access to the standard web ports.
An alternative option is to multihome the Ethernet connection. This way you can leave the primary interface attached to Apple’s services and run your third party tools on the secondary IP address. If you do this, you will still need to edit the VirtualHost directives in the apache_serviceproxy.conf file. Apple configured the service to listen on all interfaces. You will find the following in the file by default:
<VirtualHost *:80>
<VirtualHost *:443>
Change the * to the primary IP address of your server. This will ensure that Apple’s services only listen on that IP address. For example, let's say your server is currently at address 192.168.0.15. You can give it a second IP address by creating another Ethernet port in System Preferences. In this example, 192.16.0.16. Now the server will respond to both IP addresses. Edit the service proxy file and set the VHost lines to:
<VirtualHost 192.168.0.15:80>
<VirtualHost 192.168.0.15:443>
Once again reboot. When you do, Apple's service proxy will only listen on address 192.168.0.15, allowing ports 80 and 443 to be used on the secondary address 192.168.0.16. Now, you may have some DNS and port forwarding rules to modify but this will allow Apple's services (including Profile Manager) to run without surgery.
Hope this helps.
Reid
Apple Consultants Network
Author "El Capitan Server – Foundation Services" :: Exclusively available in Apple's iBooks Store
Author of Yosemite Server and Mavericks Server books