Well, evidentally, I wasn't quite asking the right question. Here's some information I got directly from Stephan on the Apache2 Bugzilla list:
Stephan said:
The bug report was about VirtualDocumentRoot and this now sets
DOCUMENT_ROOT correctly. Therefore the issue is resolved.
And I pushed back to clarify:
Maybe I missed something but I'm pretty certain I tested
$_SERVER['DOCUMENT_ROOT'] in php and it wasn't matching the value set
by VirtualDocumentRoot. You're saying it should match now?
And he replied:
Yes, in 2.4.x. It is very unlikely that the fix will ever be ported to
2.2.x because it requires infrastructure that is only present in 2.4.
So I ran apache2 -v and discovered I'm not running 2.4.x. Apache2 -v shows this:
Server version: Apache/2.2.16 (Debian)
Server built: Nov 30 2012 08:33:45
And if you notice the Server was built at the end of November this year when I used aptitude -install apache2. I don't know if apt-get would have pulled apache 2.4 instead. This is very lame. 2.4.3 stable was released in August. I don't know why aptitude pulled 2.2 but this really created a nightmare for me.
So in reality, the question I asked was moot. Everything should have worked fine, except that aptitude installed an outdated apache2 and I didn't realize what was going on. There is no bug anymore.