If you look at it closely, if you move your x scrollbar after the modify, it shows up. This is an update problem, and here is a code trick (hack) to make your script work. It forces the TableMatrix to run thru it's cells and update them. Shown 2 ways.

$top->Button(
    -text=>'modify', 
    -command=> sub {
        
        $stuff->{'3,3'} = 'asfasf';
        #&TMRefresh($tg);
            $tg->configure(-padx =>( $tg->cget(-padx)));
    },
)->pack;

Tk::MainLoop;

sub TMRefresh {
    #Required input TableMatrix object.
    #use to force matrix to update, a code trick
    return if (!$_[0]);
    $_[0]->configure(-padx =>($_[0]->cget(-padx)));
}
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