The init.d script has hardcoded paths to the run (or at least the pid-file) and log directories, the configuration of apache is also tied to /etc/apache2. With having everything in conf.d you start start 2 Apaches without playing around with the init script. Reproducible: Always Steps to Reproduce: 1. 2. 3.
i've done this to a limited degree, in CVS as apache-2.0.48-r2 now.