Isn't the batch size the target batch size used for planning the recipe?
There are always have some variations in the brewing process that all add up to various losses from when you start and to the actual bottling: different flocculation of the yeast, a less efficient whirlpool, more / less trub, dry-hopping, moving to secondary fermentation etc.
You can't add all these in the equipment profile and expect the exact same result every time but we do add the values in each brew log.
In my view the carbonation calculation should be based on the "measured bottling volume" instead of the "batch size" since it is this volume that will be carbonised.