Such as Chiltern being able to build an underpass in a fraction of the time and cost, after being told "not feasible".
Or renewing track with steel sleepers when the local PTE had expressed a serious interest in funding a third rail project over the line.
Or going all in on crackpot political infrastructure schemes that cause, rather than solve, problems.
Chiltern have undertaken a number of projects, large and small, because they've taken on the financial responsibility for the Schedule 4 and/or Schedule 8 payments themselves, they've also re-worked their own timetables to provide more generous engineering possessions windows, and they have the benefit of a route largely to themselves, so they don't have much in the way of payments outside of the business anyway.
There are similar examples of this elsewhere, Network Rail and First ScotRail (at the behest of Transport Scotland) got together and waived Schedule 4 payments for the Paisley Canal electrification, First Group did an internal deal with themselves and provided 'at-cost' ticket acceptance on First Glasgow buses during periods when trains weren't running, First ScotRail themselves again re-profiled the timetable to provide more engineering access.
That, like Chiltern's works, turned out really well, because the route was only in use by ScotRail at the time (Hawkhead oil terminal being OOU) - it's not anything like as simple with busier routes where several TOCs need access, when engineering windows are dictated by getting the first trains of a depot for ECS and getting the last trains back on a depot for ECS, particularly if you need to fuel them too. The complaints and objections to possession planning are often infuriating, and it wouldn't be the first time a TOC rep turned up complaining an additional possession was needed to undertake some work, complaining about why it couldn't have been done during a previous possession only to have to tell them their predecessor at the TOC objected and it was reprofiled.
Steel sleepers - just checking, was this before or after there was a moratorium on further third rail installations ? I don't particularly like steel sleepers and think they've been poorly deployed by NR in several instances, but DfT wanted cost savings and steel sleepers did the job...
Talking of DfT, there's no way NR can avoid crackpot political infrastructure projects. Spending for the sake of spending, because there's nothing else money can be spent on in a specific location has afflicted the railway for 70 years and will continue to do so. It's a tool too often to buy votes for the incumbent party and/or MP. You just have to try and make sure the money being spent isn't wasted, even if it doesn't strictly need to be spent.