ProductMatrix SKU has all the features of the standard ProductMatrix plus it can filter based on the products SKU.
To use this functionality you will need to make a shipping group called "SKU" (Case Sensitive!) and assign this to the products you want to filter based on their sku.
You should also set the switch in the ProductMatrix settings entitles "Use SKU as package id" to yes.
Then in the CSV file you should enter the products sku as the shipping group. The extension will now use the products sku for any product assigned to the group SKU, otherwise the standard functionality will be retained.