I don't think that the \G is really necessary.

use strict;
use warnings;

use Data::Dumper;

my $kmlfile = <<'EOD';
<coordinates>1.0001,2.0002,0 3.0003,4.0004,0 5.0005,6.0006,0
7.0007,8.0008,0 9.0009,10.0010,0
</coordinates>
EOD

my $rxCoord = qr
   {(?x)
       (?<=\s|>)
       (\d*\.\d*,\d*\.\d*)
       (?=,0)
   };
my @coords = $kmlfile =~ m{$rxCoord}g;

print Data::Dumper->Dumpxs( [ \ @coords ], [ q{*coords} ] );
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The output.

@coords = (
            '1.0001,2.0002',
            '3.0003,4.0004',
            '5.0005,6.0006',
            '7.0007,8.0008',
            '9.0009,10.0010'
          );
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I hope this is of use.

Cheers,

JohnGG