I totally agree with you. That is the way I would set up the calculations, but not the way they are currently done and I suspect that it would take a major rewrite to switch from BH to Mash efficiency for the basis of the calculations.
I have tackled the issue by making my batches with a set amount of loss to trub and chiller which covers my most hop laden recipes. I aim for 10 liters in the carboy, and 1 liter of trub loss. Even recipes with over 112 grams of hops (think 7 ounces in 5 gallon batch if you are stuck on the English system), I don't get more than 1 liter of loss to trub and chiller and most of the time it is well below that figure. In the end, I allow my volume to the carboy to float between 10.0 liters and about 10.6 liters depending upon the recipe, protein loading from the grains and hop charge in the kettle.