
Hi Emily,
I found the reason why this user had all these permissions. The customer was using the tool ShareGate. There is an rather scary option in ShareGate (IMO) to gain automatically Site Collection admin permissions.
The user did not removed his permission.
I was able to get an license and reproduce this. I removed the user with the same tool. So I would thank you for your help. I will certainly use you part of the PS script if needed.