We are not on the same page.
I'm not talking about the actual brewing process. I'm only talking about how I believe, from quickly checking some numbers, the software calculates the (rough) pre-boil estimate when you target fermenter. Not about actual losses or efficiency.
To expand:
It looks like the calculation uses the same stuff as here:
http://www.brewersfriend.com/dilution-a ... alculator/
From that they need starting and ending volumes along with gravity to estimate the pre-boil gravity. If they do that calculation using the other numbers they have there, namely: pre-boil volume, ending volume (in fermenter) and estimated ending gravity the pre-boil gravity will be off since your volume will be off with however much is left in the kettle. The ending kettle volume needs to be used instead, thus if they pull the kettle loss value from the equipment profile they can get an estimate that is much better.
Consider these rounded numbers (plug them into dilution & boil off calculator):
1.080 gravity (post boil, from recipe, grain, efficiency etc.)
7.5 gallon pre-boil volume.
5.5 gallon targeted in fermenter.
1 gallon/hour boil off.
1 gallon kettle loss.
Brewersfriend will currently estimate the pre-boil gravity to 1.060, that is off by 0.010 points in this scenario.
If you switch the target to be kettle, and enter mash efficiency instead of brewhouse then the number will be correct because of how they do the calculation.