With my kettle/stove the water calculations seem about right:
3 gallon batch
0.7 gallon absorption
1 gallon evaporation (your evaporation may be more or less)
.5 gallon kettle/fermenter trub
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5.2 gallons
You could have made the extra .010 in wort gravity by doing a batch sparge or a dunk sparge in a side pot.
Next time, if you have an extra pot, put 3.2 gallons in main pot and do BIAB as normal, in a side spaghetti pot put 2 gallons and heat to 168. When mash is done pull bag from main pot and place it in side pot.
Crank up the heat in the main pot and stir the grains in the side pot. After 10 minutes, combine the two and let the bag drain some more into the side pot.
Check your gravity about 5-10 mins, before boil is done by pulling a sample and placing in ice bath. If your gravity is low, you can add some DME or extend the boil to evaporate more water. Delay your late hop additions until you have done this. After a few batches you will figure a way that works best for you, as there are many different routes to the same goal and no "right" or wrong way to BIAB. The goal is to hit your numbers without adding DME or extending the boil but it takes some trial and error to make it all work out with the equipment you have. Once you know your evaporation rate you can also take a pre boil gravity reading and calculate where you will be at the end of the boil. Another way is to just use a little more grain if you are always coming up short on your gravity numbers.
Also, to ferment a 3 gallon batch, I use a 5 gallon carboy, and end up with 3.5 to 3.75 gallons in the fermenter. That gives me plenty of headspace for the yeast and I'll still get 3 gallons of beer after trub/yeast cake loss. Cheers!