It's quite easy to do ... just use the name of the main window in the call to bind instead of the word 'all'.  For example:

#!/usr/bin/perl -w

use strict;
use warnings;

use Tk;


# Main program
my $poe_main_window  = new MainWindow(-title => 'Tk Binding example');

my $bg   = "green";
my $psub = sub { new_toplevel($poe_main_window) };
my $text = "New Window ('c')";
my @args = (-bg => $bg, -command => $psub, -text => $text);
my $button = $poe_main_window->Button(@args)->pack();
$poe_main_window->bind($poe_main_window, '<c>', sub{ $button->invoke }
+ );
MainLoop;

# Subroutines
sub new_toplevel {
    my ($mw) = @_;
    my $top = $mw->Toplevel(-title => "New TopLevel");
    my $lbl = $top->Label(-bg => 'skyblue', -text => "Text Widget")->p
+ack();
    my $txt = $top->Text(-height => 16, -width => 120)->pack();
}
[download]

It's the line:

$poe_main_window->bind($poe_main_window, '<c>', sub{ $button->invoke }
+ );
[download]

which binds the 'c' character only to the window $poe_main_window, rather than any other Toplevel widgets created from it.

Update:  You can get more information on binding with:  perldoc Tk::bind.