Another option, is to name your maindows in the other Tk scripts differently (like $mw1, $mw2,$mw3 , etc, then don't call MainLoop in those secondary windows, but do-one-loop manually. Its a bit more complex than fork-and-exec, but you asked for manual mainloop control.

#!/usr/bin/perl
use warnings;
use strict;
use Tk qw/tkinit DoOneEvent exit DONT_WAIT ALL_EVENTS/;

my $mw = tkinit;
$mw->Button(
    -text    => 'Test',
    -command => sub { print "Pushed\n" },
)->pack();

$mw->Button(
    -text    => 'Quit',
    -command => sub { Tk::exit(0) },
)->pack();

my $I;

while (1) {
    $mw->DoOneEvent( DONT_WAIT | ALL_EVENTS );
    if ( ++$I > 10000 ) {   #slows things down use 1 for max speed
        print '.';
        $I = 0;
    }
}
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So instead of calling MainLoop in the secondary scripts, you do

sub manual_loop_control {
$mw1->DoOneEvent( DONT_WAIT | ALL_EVENTS );
$mw2->DoOneEvent( DONT_WAIT | ALL_EVENTS );
$mw3->DoOneEvent( DONT_WAIT | ALL_EVENTS );
}
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in a timer in your main Tk script, like

$mw->repeat(10, \&manual_loop_control);
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Using this method, you can even combine Gtk2 and Tk (any event loop script) and run them simultaneously.