I never did finish installing Apache 1.3.20 (I realized that 1.3.14 was fine for me) so I am not sure if that is correct. The reason why I gave up with the installation was for a reason similar to this. For some reason Apache is now wet to detect the OS you are using and install all of its components where it thinks they belong. Essentially this will mean that if you compile and install it on its own without feeding it any other commands it will simply replace your existing installation, but I am not totally sure. In my experience, it will override the arguments that you pass it during the configuration and use the default "Darwin" layout.
What I can say is that you probably can't use that server root. Since that is a place in the file system reserved for config files, etc. I don't think that the "www" user (what the web server runs as) will be able to read it or, at the very least, interact with it correctly.
From what I can tell, this will be where the config files will be kept, and nothing more.
Good luck,
Jeff.