Divides an array of different products weights to packages containing at most $package_max_weight weight and $package_max_items items. You could use this function to calculate shipping based on package weight instead of product weight.

product_weights_to_packages.php

<?php
/**
 * Divides product weights into packages.
 *
 * @param array $weights
 *   An array of product weights.
 * @param int $package_max_weight
 *   The maximum weight of a package. Set to 0 to not allow limit per weight.
 * @param int $package_max_items
 *   The maximum number of items per package. Set to 0 to not allow limit per items.
 *
 * @return array
 *   An array of package weights.
 */
function commerce_shipping_packages_product_weights_to_packages($weights, $package_max_weight = 0, $package_max_items = 0) {
  // Sort weights from maximum to minimum.
  rsort($weights);

  // An array to hold the packages.
  $packages = array();

  // An array to hold the parsed weights.
  $parsed = array();

  // A variable to hold the package's weight.
  $package_weight = 0;

  // A variable to hold the package's total items.
  $package_items = 0;

  // Get the latest (equivalent) key.
  end($weights);
  $eqweight_index = key($weights);

  // Latest PHP versions don't need this since foreach automatically resets.
  reset($weights);

  foreach ($weights as $index => $weight) {
    if (in_array($index, $parsed)) {
      // Reached an already parsed value. Assume all values were parsed.
      if ($package_weight > 0 && $package_items > 0) {
        // There are still items without a package.
        $packages[] = $package_weight;
      }
      break;
    }

    if ($package_max_items) {
      // Check number of items in package including this item.
      if ($package_items + 1 > $package_max_items) {
        $packages[] = $package_weight;
        $package_weight = 0;
        $package_items = 0;
      }
    }

    // Check package weight including this weight.
    if ($package_max_weight) {
      if ($weight > $package_max_weight) {
        // This item is already heavy enough. Create a new package for any
        // previous items. Create a new package for this item too.
        $parsed[] = $index;
        if ($package_weight) {
          $packages[] = $package_weight;
        }
        $packages[] = $weight;
        $package_items = 0;
        $package_weight = 0;
        continue;
      }
      elseif ($package_weight + $weight > $package_max_weight) {
        // This package already contains heavy enough items. Create a new
        // package for them. Then add this weight as a package base weight.
        $packages[] = $package_weight;
        $parsed[] = $index;
        $package_items = 1;
        $package_weight = $weight;
      }
      else {
        // This item can be stored in the current package.
        $package_weight += $weight;
        $package_items++;
        $parsed[] = $index;
      }

      if (isset($weights[$eqweight_index]) && !in_array($eqweight_index, $parsed)) {
        // There is a non-parsed equivalent weight.
        if (!$package_max_items || $package_max_items && $package_max_items > $package_items) {
          // No package max items configured or didn't yet reach max items.
          if ($package_weight + $weights[$eqweight_index] <= $package_max_weight) {
            // Haven't yet reached maximum weight.
            $package_weight += $weights[$eqweight_index];
            $package_items++;
            $parsed[] = $eqweight_index;
            // Decrease the equivalent weight index key by 1.
            $eqweight_index--;
          }
        }
      }
    }
  }
  return $packages;
}