Others are experiencing the same persistent pop-ups.
There are indications that eBay is fixing the issue, but it may take additional time or signing out of eBay and restarting the browser before the changes are effective.
You may be able to use an ad blocker's element hiding tool to temporarily block all notification popups on eBay, if you are using a desktop browser.
Most desktop ad blockers have a point and click interface to allow users to block certain page elements from displaying. With a little trial and error you may be able to block those notifications completely in one browser, then disable that ad blocking rule once eBay fixes things.
