Use a timer to destroy the mainwindow. If you need the script to continue on, destroy the mainwindow, instead of exiting, then you can run more commands after the Tk window is gone, leaving you with the default answer.

#!/usr/bin/perl
use warnings;
use strict;
use Tk;

my $choice;

my $mw = new MainWindow(-height => 600,-width => 600 ,-title=>"Message
+"); # Main Window

$mw->overrideredirect(1);    # Remove window manager controls
$mw->geometry('+700+650');

my $frm_name = $mw -> Frame() -> pack();

my $lab;
if ($ARGV[0] eq "-A"){

$lab = $frm_name -> Label(
    -text=>"D[$ARGV[1]]\nClick 'Ok' To start the Process",
    -anchor => 'center',-height => 5,-width=> 55 ,
    -foreground => 'blue',
) -> pack();

$mw -> Button(-text=>"Ok", -command =>sub { 
     my $status = $mw -> messageBox(
      -message=>"Do u want to start the process..?",
      -type=>'yesno',);
     
     if($status eq "Yes")     {
         $choice = "Yes";
         print "$choice\n";
         exit;
       }else{
        $choice = "No";
       }
    }
) -> pack(-side =>'right',-expand => 0); 

$mw -> Button(-text=>"Cancel", -command =>sub { print"cancel"; exit;})
+ -> pack(-side
    =>'right',-expand => 0 );

}


my $timer = $mw->after(5000, sub{ $choice = 'No'; print "$choice\n"; $
+mw->destroy; } );

MainLoop;

print "after mainloop exits-> $choice\n";
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