Set the RewriteBase configuration in the .htaccess by default
Apache server does not allow modules to reconfigure the DOCUMENT_ROOT, this can cause problems with mod_rewrite, and will cause problems with mod_vhost_alias.
This is fixed in a recent commit of apache, but can still affect a lot of installations. AFAIK it does not hurt to set the RewriteBase directive by default, so it might be worth to set it.
Apache commit which fixes this in apache: http://svn.apache.org/viewvc?view=revision&revision=1132494