Unfortunately, the https://www.drupal.org/project/commerce_pricing_attributes module and it's brethren (product options and product attributes) are a part of what I like to call the "hunziker approach." This removes the idea of separate SKUs per attribute. Which has the unfortunate effect of giving the masses what they expect and distorting/side-stepping a very deliberate separation of logic in Drupal Commerce. It would be like forcing Views to store taxonomy terms. It might make your task easier, but it is not the right approach.
The "hunziker" approach to Drupal Commerce is not supported nor recommended by the creators of Drupal Commerce. Thus, any problems you might have with the modules is "by design" unfortunately.
If you want attributes to update the pricing correctly, try creating separate product entities with unique and single attributes and attaching them to one single product display node.