Yes, that is where you lost gravity points.
I use Brewer's Friend, and I set the batch size to 5.25 gallons, and the boil size to 8.25 gallons. The reason is that I am going to boil off 1.5 gallons, so my end of boil volume is 6.75 gallons. My boil kettle has a 1.5 gallon loss that accounts for break and hops debris. That leaves me with 5.25 gallons of clear wort going into the fermenter.
The extra .25 gallons going into the fermenter accounts for the yeast cake at the end of fermentation. My goal is to package 5 gallons, or 54 12oz bottles. In some cases with session ales I can rack 6 gallons into the fermenter, which I consider to be bonus bottles, maybe filling a few more than 54 bottles.
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