Cross-wiki notifications represent a bucket for "more notifications from other wikis". So even if there are recent ones there we want to keep the unread notifications from the current wiki on top. This will allow users to avoid getting distracted but what is going on on other more active wikis if they chose to focus on a specific wiki first.
As shown in the screenshot below, this is not happening. The cross-wiki bundle is expected to appear below the other unread notification.