I'm setting up shop and am testing the cart for shipping charges. I'm using shopify shipping, have my "saved packages" set to USPS Priority Mail Padded Flat Rate Envelope. I don't have regular priority boxes enabled. I'm on the east coast. When I put in a test order to check the shipping charges, they look ok for the east coast. When I test an order going to the west coast, it's not reflecting the flat rate cost. It looks to be giving me the regular priority cost to the west coast, which is much too high.
Ideally if you have selected Flat rate box for shipping, there is no way the cost can change for west coast. This is because flat rate boxes are the same throughout the country irrespective of the state you are shipping to. In your case, due to some reason or the other(maybe dimensions are matching), the package is not getting packed in the USPS Priority Mail Padded Flat Rate Envelope and as a result default weight based calculation is happening. effective monitoring of packages and rates can happen with a transparent app that shows the complete transaction including the weight and dimensions of the package that is going. You can try the Multi Carrier Shipping label app for this purpose.