Because they had their END block already called and within closed files or dropped connections

That's why I said you have to make sure the module is loaded before your END block is compiled. The order in which END blocks are executed is well defined.

Now it's true the module can shoot itself in the foot — Perl sure has plenty of ways of making that happen — but it can do that whether you use END blocks or not. It's not something you should worry about until you encounter a module with which you have an issue.