So 2 years later, this is still an ongoing issue, right? 
We have the same problem. Our store offers several currencies, and in our storefront and at the checkout, they are all displayed in the format: $12.50 USD. This is not correct for some currencies such as the Euro which is displayed as €12.50 EUR when it should be 12,50 € EUR.
If it can help some dev (I am not) to find a fix, I believe this article could help.