I think you might want to use the base shipping with the shipping cost to avoid charging extra per product.
Say, You have a physical product of $10.00 and you are using a base shipping cost of $10.00 for this product. As you are using a base shipping cost, you don't need to specify the full shipping cost for country A, Country B, Country C, Country D and Country E in the variation. In the variation You will specify the extra costs (which together with the base shipping will make the full cost) that you need to charge for different countries. Have a look at the following variation example -
Variation 1: Shipping
Country A $2.00
Country B $5.00
Country C $7.00
country D $9.00
country E $11.oo
In the above variation, if your customer choose country A it will charge extra $2.00 per product for shipping cost with a base shipping of $10.00 ( base shipping $10.00+ $2.00 = total $12.00 shippping cost for country A). Now if that customer add 2 products to the cart , the total shipping cost will be $14.00 ( base shipping 10.00+2*2 = $14.00). If you've used a flat $12,00 shipping cost in the variation it'd add $12.00 everytime you add the product in the cart. Hope this makes sense.
You can also have a look on the following post to clarify this -
http://www.tipsandtricks-hq.com/ecommerce/how-the-shipping-cost-calculation-works-in-wordpress-estore-50