Presumably a complete timetable redraft would be required to avoid this?
The issue is that Maghull North had to have an extra unit added - it only just worked before, and with the extra stop it didn't any more. I think it's 6 units rather than 5 now? That I guess means deliberately slowing it down to avoid that problem.
I wonder if a permanent change to the Hunts Cross being joined to the Ormskirk would help sort that out (it doesn't overly matter which it is in passenger terms because hardly anyone travels through across Liverpool). Southport has three electrified platforms (I think) so has more flexibility.
The other thing that would sort it out would be the proposed extra station near the Eldonian (between Moorfields and Sandhills), but that's gone quite quiet.
But I think this point answers the Aughton Park/Town Green question - if you skip stopped them you'd just wait those two minutes outside Ormskirk, so there's no sense in doing so. Though they have done it during the Aintree Races to make tighter diagrams with Aintree shuttles work.