I am somewhat lost with all the volumes and gravities given. But, collecting the proper volume is critical. If the recipe calls for a final volume of 3 gallons and you are collecting 3.5 gallons your gravity will be low. I think you may be accounting too much to trub loss. I lose less than a quarter gallon to trub in a 5 gallon batch. I do use a 5 gallon paint strainer bag to contain hop debris.
Keep adjusting your volumes until you end up with the predicted amount of wort going into the fermenter without leaving much if any in the boil kettle. I leave only the thickest part in the BK, less than 12 ounces.
I believe you're onto something! I've never done one of these 3 gallon BIAB kits before, but I just looked up the instructions on the NB website. While I didn't find it directly stated, if these kits are designed like every other kit in the world, they are meant to put 3 gallons into the fermenter.