Virtual Host Config files that rewrite themselves...

You're not the only one to tussle with this.

While details of what particular "special" configuration is required here might help tailor this answer, in general you have some obvious choices:

1. Conform to Apple's norms when directly modifying the configuration files (and generally using Server Admin or Server.app tools) and avoid modifying the configuration files
2. Not using Server Admin nor Server.app tools (somewhat risky, as updates can access these files)
3. Using an operating system platform that more directly supports your requirements (probably the best approach); there are OS platforms available that specifically support these sorts of customizations and configuration modifications.
4. Change your requirements to match what OS X Server provides.

With details of what you're doing that's different or special or not supported by the current tools, you might consider logging some specific enhancement suggestions with Apple for consideration and potential inclusion in future releases of the tools.

You're not the first person to slam into this wall, err, this difference in management interfaces and server management style. I certainly slammed it, too.

With your present management preference, you're going to be pounding against how Apple configures OS X and OS X Server and how Apple expects the OS to be managed, and that's not going to be "fun". As you've discovered. Otherwise, you're (often) going to have to "let go" of the use of the configuration files and related management interfaces.

Partiocularly around Apache and its configuration files. Various components of OS X Server modify those files "themselves".

Loading Linux or one of the BSD variants and using that might be a much better fit for how you prefer to operate and manage your server. I have some "weird" boxes around for this reason; for tasks that OS X Server just isn't good at.

For the available documentation, see the OS X Server Snow Leopard Server 10.6 documentation set for most of what's available. The Lion Server documentation is not as extensive as the Snow Leopard Server documentation. It is possible to step beyond what Server Admin and Server apps allow, but there's little specific documentation around the conflicts. As should be obvious: I'm not aware of any specific documentation around what you can "get away with" here, beyond the manuals and beyond (careful) use of the defaults command and various plist files.

You haven't provided details on what you're doing with the Apache configuration files (beyond setting up a Diaspora pod, and I haven't experimented with that), nor with what particular sort of "gibberish" arises here. If you're using a shell-level ASCII-based text editor (nano, vim, emacs, etc) (and not a GUI-based or Unicode-based or other editor), then the usual behavior of Server Admin and Server.app would be to revert the Apache files to their previous state, or to get confused.

While providing full access into the configuration files through a GUI tool and preserving the settings is a good goal for a more advanced user, it's also a massive undertaking, particularly if you're trying to avoid (as Apple is) a massively confusing management interface. Apple substantially simplified the management interfaces with Lion Server and removed a number of options and knobs, over what was available in Snow Leopard Server, too.