Hi,
By convention, the ingredients are driven by your overall brewhouse efficiency which is intended to represent the end-to-end efficiency of your system. If you have significant losses that should give you a lower overall efficiency.
I'm working on an alternative system (optional) to start with mash efficiency and then take into account all the losses from there on out. I think this is what you would prefer to see, which is why I have it planned for a future version. However, most brewing programs quote overall brewhouse efficiency and not mash efficiency, so it would still require you to know your mash efficiency going in.
Thanks,
Brad