Since this post has been posted quite a long ago, I would like to update it since it might help anyone landing on this thread.
Although Shopify allows you to adjust the box dimensions now, it does not handle the rates based on the product dimensions. Shopify only takes the weight of the product while calculating the rates, which is why the rates might go high in case of products that are mentioned here. So, to calculate the rates based on product dimensions and pack the products accordingly, you will have to use a Shopify FedEx app. Using such apps will not only help in calculating rates based on the weight and dimensions, but also in automating the packing process based on the dimensions of the product.