I tend to think of global variables as "omnipresent variables". Variables contain data, and should be scoped to the smallest enclosing block where the data is being used. Sometimes, it just makes sense to have data available everywhere. Whether the program is running in debugging mode for instance. Or access to the toplevel window of a program.
Sometimes it saves a lot of typing (and some schools say the smaller the program, the less bugs it contains) to have an omnipresent variable than pass the variable around to almost every subroutine you call.
But if you prefer simple rules and don't want to spend a few braincells wondering whether it makes sense to deviate from a guideline, you can always do:
package main;
my $MW = ...; # Create your main window here.
sub UNIVERSAL::MW {$MW}
After all, subroutine are (global) variables as well - but noone ever yells at you for using them.
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