Use the --with-layout=[F:]ID option to select a particular installation path base-layout. There are many layouts pre-defined in the file config.layout. Except on MacOS(X) configure defaults to the `Apache' classical path layout. You can get an overview of the existing layouts by using the command:
Especially annoyingly, the default layout partially ignores the --prefix argument, and seems to put a bunch of stuff in /Library. Outstanding!

You installed an updated Apache? The OS comes with it already installed.
I wanted to install one that I controlled in my own directory.