Mysql – Why is the phpMyAdmin page not interpreted from raw PHP code

The config you have posted is vastly more complicated than it needs to be. I'm not quite sure why it's set up that way, but I did notice a few things that might make a difference.

First and foremost, in drupal6.conf all you should need is the following:

<Directory /home/d/r/drupal/web/public_html/>
    Options +FollowSymLinks
    AllowOverride All
    order allow,deny
    allow from all
</Directory>

The rest of the stuff is secondary and may be complicating (or causing) the problem. I'd recommend - especially for the initial install - to simplify the configs as much as possible. I run a lot of Drupal sites and I never mess with anything beyond pointing the mysite.conf to the Drupal directory and creating the (Drupal root)/sites/my.site.com directory and settings files.

I'd recommend ripping all the other stuff out of the drupal6.conf and seeing if it works for the install. Then add back in the access blocks on the /admin, install.php, etc. I don't recommend messing with the .htaccess files in the config file. Leave out the line including the .htaccess in the apache configs and just let .htaccess be picked up as it's designed to by apache.

This is most likely that the index.php (or whatever) inside /usr/share/phpMyAdmin isn't being opened by default. See what's inside that directory and then try specifying the file directly to see if that fixes it (we can fix the issue afterwards).

If not, it could be a permissions issue (it's unlikely): Find out which user is running apache:
sudo ps aux | grep "apache2" | cut -f1 -d" "
There will be a couple of roots in there, ignore those and pick the other username. Then try:
sudo -u whatever_user_that_was ls /usr/share/phpMyAdmin
If that gives permission denied, that's your problem.