All services (2 per hour) from Atherton go towards Victoria, from Bolton, 5 per hour go to Castlefield (and 3 per hour go to Vic).
They're going to need to cross over somewhere.
What I'm saying is that trains could occupy both platforms, which would allow for a shorter delay for whichever has to be held before entering the station. This is instead of the current scenario where a train is held for a fair bit (and I've been on trains held for near enough 10 minutes), to allow one on the other route to come through and spend however long on the platform.
It could also reduce lateness for anything running late behind another train. If one train is running late, you could have two trains within a couple of minutes from Bolton - this would avoid the scenario of one train being further delayed by being held whilst the first one is on the platform.
The loop south of the station could allow for trains to head towards Piccadilly from the Atherton line. I know all services from there go to Victoria, but it could allow for a future change (once Wigan - Lostock electrification is complete) allowing an Atherton service to head to Oxford Road, Piccadilly or the Airport, or allow any freight movements to shoot through.
The other option would be to build a loop from the up Atherton line across onto the up fast, which would allow for those services to tuck behind the service from Bolton, should that occupy Platform 1 (and heading to Piccadilly).
I'm probably vastly over-thinking it!