One way to do this is to capture the junk along with the substrings

This is a fine use for the special treatment of capturing parentheses in the first (regex) argument to split:

  my @chunks;
  my @start_pos;
  my $pos = 0;
  foreach my $chunk ( split /(X+)/, $string )
  {
      unless ( $chunk =~ /^X/ )
      {
          push @start_pos, $pos;
          push @chunks, $chunk;
      }
      $pos += length $chunk;
  }
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