the my @A assignment uses the values of $x and $y at that time, and then you get an AoA of static numbers .. changing $x and $y after the fact will have no effect. I believe what you're looking for is a function, so you can pass in $x and $y and get back the array calculated for those two values.

sub makeBoxArray {
  my ($x, $y) =  @_;
  return (
   [ ([$x, $y  ]), ([$x+1, $y  ]), ([$x+2, $y  ]), ([$x+3, $y  ]) ],
   [ ([$x, $y+1]), ([$x+1, $y+1]), ([$x+2, $y+1]), ([$x+3, $y+1]) ],
   [ ([$x, $y+2]), ([$x+1, $y+2]), ([$x+2, $y+2]), ([$x+3, $y+2]) ],
   [ ([$x, $y+3]), ([$x+1, $y+3]), ([$x+2, $y+3]), ([$x+3, $y+3]) ],
  );
}

my @A = makeBoxArray( 5, 10 );
# use @A for something
@A = makeBoxArray( 7, 2 );
# use @A for something
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To take it a step further, the array can be generated using map to eliminate the repetitive text, and also add optional params for the box size:

sub makeBoxArray {
  my $left = shift;
  my $top = shift;
  my $width = shift || 4;
  my $height = shift || 4;
  return map {
      my $y = $_;
      [ map { [$left+$_, $top+$y] } 0 .. $width-1 ]
    } 0 .. $height-1 ;
}
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