Does TL have the same level of interworking between the branches? I thought they were much simpler diagrams, which even with the long through services and congested centre must make it easier to unpick problems.
IOW, the problem is less that there are through services and more that units and crews are coming and going to all sorts of destinations so you can't simply bring everything back on time by cancelling a round trip and stepping up.
Generally, everything (rolling stock wise) is on self-contained circuits most of the day. E.g. trains just ping back and forth between Cambridge and Brighton, with decent turnround times at both ends to recover late running. There are a few quirks in the peak (e.g. trains starting from Horsham go to Bedford in the morning peak, then Peterborough thereafter) but otherwise it's fairly 'set' and standardised.
I think train crew is intended to be fairly simple too, with limited mid-route crew changes and drivers working end to end as far as possible.