You can go through the trouble of changing the port (to anything really, but the standard https port 443 jumps to mind), but you'll have to modify the configuration files with every release. It's easier to have a dedicate machine, or VM, for your JSS/mySQL database.
Personally, I think you should take a step back and really think about whether you want this installed on Apple hardware. Xserves are out, unless you like getting replacement parts from eBay. Mini's really aren't true servers unless you're a very small shop. And, unless your server room guys are very lenient, they will not be happy with a MacPro in the server room.
I think, in the long run, you'll be happier with some flavor of Linux (or Windows if you're a Windows shop) running your JSS and then leveraging whatever network filer you currently have in place for the distribution point(s). It's easier to do in the beginning rather than later on. It also has the benefit, in most enterprise environments, of shifting the server maintenance pieces of managing a JSS to a group of people that manage a bunch of other servers. This lets you, or whoever will be doing it, focus on managing the Macs.
Also, have the clients point at a DNS CNAME. Your server will (eventually) die, it's easier to change a DNS record to point at a new server then to tell all the clients to point at a new server.
My 2¢