Most of the recipes are for 6 gallons, with the assumption that 1 gallon will be sucked up by the hops. This will be an even bigger problem for you because you are doing a partial boil (so the hops will suck up higher gravity wort). Even at 70% efficiency and no loss to the hops I only get 1.054 for your OG (it would take about 9 lbs of LME total to get you there). Maybe you have the software set to a 3.5 gallon batch?
You'll also have a problem getting the beer bitter enough since you'll saturate your 3.5 gallon boil with 100 IBUs and then dilute to 5 gallons and only have 70 (and that is only if you finish the boil with 3.5 gallons of wort in your fermenter). You should consider doing two boils (brew half the batch, then the other half later or the next day), so you can get better hop utilization, lose less gravity, and keep the color lighter.