Some people focus on hitting the right volume for the batch (often what's packaged). As indicated above, that's often a batch sized to leave enough after yeast loss to exactly fill a keg (or whatever container).
Others, like myself, worry less about the batch volume and more about the gravity.
The way I look at it, losses to trub, yeast, and hop matter are all recipe dependent. An Imperial IPA with 1.5 lbs of hops is going to lose a lot more wort/beer (including with dry hops) than a Doppelbock will. And there I just prefer to let experience be my guide rather than letting software muck with it, because software never gets it right, and usually throws off my gravity as a result. So for me, batch size is the post-chill volume. As in, what's left in my kettle after chilling with my immersion chiller. This way, I'm able to dial in my gravity to a point of being exactly on every time. If I lose an extra bit to trub, no worries. I'll just account for that later.
Point is, decide what's right for you.