The idea behind running the headphone out for the sub is that having the pre-outs running two sets of wires at the same time and into 2 amplifiers at the same time is harder for the dac to power than a single set of wires and amp. Running from the headphone amp to the sub would, I think, reduce that because the headphone amp is its own separate amplification from the preouts. And it's something you can try for the cost of a $5 headphone jack to rca adapter.
IMO it's a mistake to not try a regular preamp with the Benchmarks. While there may be a tiny loss of transparency I found a preamp was overall a pretty big improvement.