Take a look at the headinclude template:
HTML Code:
<vb:if condition="$vboptions['storecssasfile']">
{vb:cssfile main-rollup.css}
{vb:raw template_hook.custom_css_links}
<vb:else />
{vb:cssfile bbcode.css,editor.css,popupmenu.css,reset-fonts.css,vbulletin.css,vbulletin-chrome.css,vbulletin-formcontrols.css{vb:raw template_hook.custom_css_list}}
</vb:if>
There is an if/else there. You can only use the template hook custom_css_list if the css is not being stored in the file system. So, two different template_hooks need to be defined.
PHP Code:
$template_hook['custom_css_links'] .= xxxxxx;
$template_hook['custom_css_list'] .= yyyyyy;