Ninja i checked too, but with the protostar as default template, the system message is displayed, but with purity iii not.
**Tried it yourself: **
Publishing a module on position sidebar-2 then the <div id="system-message-container"> disappears from the source of the template.
Disabling this module on position sidebar-2: then <div id="system-message-container"> is there.
Regards,
Peter