fossil breaks end portal

In ibxtoycat's video this fossil stops you beating minecraft a fossil had broken a end portal block. this would make you not able to beat minecraft. I know a simple way to fix it: make strongholds the last thing that generates. so instead of the fossil overwriting the strong hold the strong hold over writes the fossil. Here is a link youtube.com/watch?v=cd4k-ERP1cw&t=0s