This *should* be taken into account, as overnight workings still tend to work from or to a stabling point at some point. The GTR overnight services should certainly be taken into account on my list.
The list essentially covers overnight berthing only, or as you mentioned daytime berthing for overnight services. Inter-peak berthing is not included, though there probably aren’t many examples of stabling points which are used inter-peak but not overnight. Camden Carriage Sidings seems to be one such example, in this case for LNwR.
Incidentally the current timetable includes overnight berthing for TfW at Aberdare, Merthyr and Pontypridd. I presume this is temporary as part of the metro conversion works.