This is a perception, and not reality.
There are only 5 types of timing allowances, and three of them (engineering time, pathing time, and adjustment time) are there to make the timetable fit together and in the first case to allow for temporary speed restrictions. There is more pathing time now than there used to be, but that is a function of there being more trains on the network.
The other two allowances are 1) performance allowance, which is designed to allow for minor delays that could reasonably be expected but the location of them will vary (eg all trains in the Welwyn viaduct area get a minute of performance allowance, and have done for a long time), and 2) public differentials, where the arrival time is advertised to passengers later than the working timetable. This latter one is the only one that can be reasonably said to be ‘padding’, and the amount of it in the timetable as a whole has fallen by almost 70% in the past few years.