Skipping Birkdale is more mismanagement than a mystery. The stopping pattern was decided by someone who doesn’t understand the infrastructure. In the northbound direction, not stopping at Birkdale actually increases the signallers workload because there isn’t much time to close Aughton Road level crossing via CCTV.
Stopping at both Blundelsands & Crosby and Waterloo which are right next to each other, rather than e.g. Bootle New Strand or Ainsdale was a bit of a mystery though. If a slightly reduced journey time could run an hourly service with only a single unit or 2, then it might make sense, but I’m assuming the choice of stations doesn’t make any difference to the journey time unless they need to time level crossings so attention can be given to Maghull etc.