When the WCML underwent a wholescale re-write with the introduction of 125mph tilting trains, as part of the West Coast upgrade programme, there was a dedicated team of experienced timetablers who beavered away for many months to craft an entirely new timetable. One of the major inputs to this was where would the engineering allowances "box time" be, and at what values. Three-way discussions took place, chaired by DfT, with NR determining the engineering / maintenance requirements, and the TOCs inputting when required to state what flexibility they had especially late night / early morning.
The actual values are determined by estimating the amount of work scheduled to take place in a given area, and an estimate made for the probable impact of any temporary speed restrictions resulting from this.
In principle it is better to spread a number of low values across the route rather than having it all in one lump near the end of the journey. In the 1980s it was often the case that trains would arrive Euston very early, particularly Saturday daytimes when there was no engineering work scheduled (all the crews resting prior to dismantling everything on Sunday). Conversely, with daytime patrolling blocks scheduled which involved weaves onto the slow lines, the engineering allowance could be insufficient, resulting in delays and congestion.
The location of the engineering allowance is also critical, especially as the network capacity gets used up. As an example, running from Euston via Northampton there would be a batch of recovery time approaching Rugby, to ensure timely presentation at this key junction. However once Daventry freight terminal opened it meant that trains were departing Daventry on time and then encountering unnecessary "box time", sometimes to the detriment of their onward path down the WCML. In the following timetable the engineering allowance was moved south of Daventry, resolving the issue.