If you are mining for your own resources then how can it be selling at a loss? The OP may not be making as much coin as they could with higher prices and this may prove to be frustrating for shop owners that buy everything and then craft it, but in no way is the selling at a loss.
I think in general this is a good thing and part of how an economy works. Every player is going to place a different value on their time and if more shopkeepers charge less because they are actually gathering their own resources, then I am all for it. When I need coils, I certainly know who I am going to ask