Feature request: In case there are dependencies between the modules loaded from /etc/httpd/conf.d, I will recommend you put two-digit number prefixes on all .conf files to ensure they are loaded in the correct order.
We considered this, but there aren't supposed to be load-order dependencies between modules in 2.0 due to the new hooks API. A few have cropped up since that decision was taken, of course.
I'll mark this as WONTFIX until we find a case where this is actually needed.