How to manually patch OS X Server bundled outdated components?

If you manually replace components used by the server software you are going to almost certainly break things especially Server.app (for administration) and in this case you would also almost certainly break Profile Manager and the Wiki server.

If you want to use Apple's server software then you have no real choice but like the rest of us to wait for Apple to include any upgrades.

As examples the bootpd and racoon software and even the ntp client included by Apple are not merely different versions compared to the latest stable releases but are actually heavily customised by Apple and behave significantly differently. As far as I am aware the Apache used by Apple is pretty standard and the main difference is the name and locations of files Appe uses, i.e. not only do Apple not use the standard httpd.conf file and location but the process of installing SSL certificates is very different to a standard Apache system.

It is possible to upgrade some components e.g. perl with minimal risk of break Apple services, it is also possible to install separate copies of items like Apache and run them separately to Apple's. However such a separate install of Apache would not serve Profile Manager up for you.