BeerSmith operates its modeling by using your volume of wort into the fermenter and process losses along with the brew house efficiency to determine how much sugar is liberated from the malt bill it is given and the volumes you start with. These values are set by the user in their equipment profile.
So, if you make a change in your volume losses, such as increasing the trub loss, the program responds by increasing the amount of water needed and of sugar pulled from the malt bill, thus increasing the mash efficiency to meet the target brew house efficiency.
In reality, my mash efficiency stays pretty consistent through most of the gravity range I target for my recipes and only drops off when I get to gravity targets above 1.080 or so. In order to make a process change, such as increasing my trub from 1 liter to 1.5 liters, I need to recalculate the brew house efficiency in order to maintain the mash efficiency I would expect to achieve. Then I would make a new equipment profile to reflect this change and either scale the recipe to the new equipment profile, change the equipment profile in my recipe existing in my recipe, or build a new recipe using that profile.