Since you can also see everything in CHECK and END blocks, which are run after compilation, I still don't understand what is going on.

I think it's because at those stages in the program's lifecycle you don't have a runtime scope, or perhaps it's better said that the entire program is in their scope. They see everything written on a particular pad by the compiler, without perl hiding entries according to scoping rules. (Update: see diotalevi's remark above.)