So, I have yet to attempt the fix you mentioned but conducted another test just to be sure, and I get the same incorrect values both in the store front and back end. Let me break it down to try and make it clear:

So first off - I don't know if this is normal behavior or not, but I can never actually see the discount reflected in the subtotal. The subtotal always shows as what it is without the discount, and then after shows whatever the discount amount comes out to be.

So I have the following order with the following values after the coupon:

Subtotal: 202.40
Discount: 20.24 (10%)
Shipping: 38.50
Fee 8.43
Tax: 18.62
Total: 247.71

Now, again to clarify, that 202.40 is the same before and after the coupon is applied. If you do the math, you'll see that the fee is calculated by adding the shipping and unmodified subtotal together and multiplying by 3.5%

The sales tax, however, is subtracting 20.24 from 202.40, then adding that to the shipping and (incorrect) fee, then multiplying the sum by 8.125%, which is correct (other then the fact that the fee is incorrect).

I asked diptimoy to implement the fix you mentioned so I can do some more testing, but to be clear, these results are both on the storefront and back end.