Great news, @SouIsAs - thanks for sharing!
I just updated mailcow. mailcow/sogo is v1.104 now, SOGo is still v5.3.0.
Anyway, 2FA works again although the fix was announced for SOGo v5.3.1
Sadly, all users have to re-initialize their 2FA settings. The old secret seams to be lost.
But, 2FA is working again as mentioned by @SouIsAs .