Thunderbird does not restore up from the task bar when a new email alert popup occurs, and it selected.
Previous version to 88.0 Thunderbird would restore up from the task bar, if the user selected the link in the alert popup. This now selects that email message, but no restore up occurs. I have looked through the setting for incoming emails, and this is not a setting. I believe it was broken by some code change.
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This is NOT the Notification area icon popup, but the popup just above this, with the subject of the email shown. This used to work correctly that when you clicked on it, it would restore up Thunderbird from task bar, and open that email. Sometimes there are multiple email notifications at the same time, but the one you click on becomes active in Thunderbird. If you click on the alert popup, the other email will become active to view. I wanted to clarify this.
Appears this is fixed now with version 88.0b3 beta release.