Yes, it looks like using substr instead of matching with capture is the most significant improvement to be made. In fact, changing the original to do that causes it to run faster than anything except Tri_Substr2.

sub orig_substr {
    my (@a, @b) ;
    my @temp = @master;
    foreach my $value (@temp) {
    push @a, substr($value, 2) if (substr($value,0,2) eq 'a_') ;
    push @b, substr($value, 2) if (substr($value,0,2) eq 'b_') ;
    }
    print "@a <==> @b\n" if $testing;
}
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