__Variables.html

<mt:var name="override_identifier" value="1" /> <!-- to use the override template -->
<mt:var name="override_identifier" value="0" /> <!-- to not use the override template (or just don't include) -->

sys_template.html

<mt:setvar name="blog_id" value="$blog_id" />
<mt:unless name="blog_id"><mt:setvar name="blog_id" value="$request.blog_id""/></mt:unless>
<mt:if name="blog_id">
    <mt:blogs include_blogs="$blog_id">
        <mt:include module="__Variables" global="0">
        <mt:if name="override_identifier">
          <mt:var name="override" value="1">
        </mt:if>
    </mt:blogs>
</mt:if>

<mt:if name="override">
    <mt:include module="override_identifier" global="0" />
<mt:else>

... existing template code ...

</mt:if>