To mitigate this, planning could use average (or even optimistic) dwells everywhere, then add ~2 minutes at the last stop before reaching mainlines or major stations (i.e. Bentley or Adwick in this case) to allow for any accumulated delays. This doesn't seem to be how it's done in practice, so it'd be interesting to hear how it's supposed to work.
Whilst that approach may mitigate the problem, it would require a number of very uncomfortable decisions to be made due to the reduction in available capacity, caused (directly or indirectly) by the increased running time.
Those uncomfortable decisions would include some/all of the following:
Do all services have increased overall running time? And if not, which services will/will not be impacted?
Which services could no longer be accommodated in the timetable?
Of the current services which could be only partially accommodated: Which services would have there frequency reduced? and/or; Which services would station calls taken out?
Who would pick up the tab for increased operational costs where turnround times are broken but the capacity exists to maintain current service level?
Not to mention the vast scale of work reviewing and reworking the complete timetable planning rules, the timetable, rolling stock diagrams, & train crew diagrams.