Even with the standard equipment profiles on BeerSmith, I highly recommend users take measurements and adjust the equipment profile to better reflect their system and process.
The boil size is the volume of wort collected from the mash, so it does not represent the initial strike water volume. The strike water volume is set based upon your equipment profile and your mash profile. The equipment profile helps to determine the amount of water which will be needed for the mash and sparge, the mash profile will determine the split between the amount of water used in the mash, adjusted for any dead space in the equipment profile, and the sparge water which will be any volume not used for the mash to make the difference between the total water needed and the water used for the mash.
When you scale the recipe to your equipment profile and apply the mash profile which you will use, the volumes used for mash and sparge will adjust automatically to reflect your process.