I ... usually declare/initialize variables at the top of a script.

Don't do that. It is a bad idea.

I was also doing that at my beginning in Perl, because of my C background (I think it has changed in C, but there was a time where all variables had to be declared either at the beginning of each function, or at the beginning of the program for global variables.

Declaring all your variables at the beginning of the program defeats at least a good half of the advantages of lexical variables. It makes your variable essentially global, which is precisely what you don't want to do. You should rather declare your variables in the smallest possible lexical scope (function level, loop level, block level, whatever).