It would really take quite a Mac, and quite a workload, to cause one to discharge on a 96W adapter. The full-on M3 Max certainly can when pushed - people have reported that machine can draw 120W sustained if both CPU and GPU are running full blast. Very little will light that monster up to full blast for long (much of why you want that performance is for burst power for things like photo noise reduction). Of course, you CAN cause it to stay at that power level - exporting a feature-length film would peg the power meter to the wall and leave it there for hours.
As far as I can tell, the two real reasons for the 140W adapter (both of which have some validity) are to allow reasonably fast charging when the Mac is in use in a heavy workload (it may not be easy to peg one at 120W or more for an hour, but there are quite a few workloads that will sustain 50-80 watts), and to allow full power at a low state of charge. At least the 16/40 M3 Max, and I suspect the 14/30 as well, CAN exceed 100 watts, and supplying only a 96W adapter would mean that the machine couldn't run at full power PLUGGED IN if the battery were low.
I'm not sure that either of those justifications apply as much to the M3 Pro. It has about half the processor power draw of the fully enabled M3 Max (half the CPU performance cores and just under half the GPU cores). Of course, the auxiliary draws are closer - it has less than half the RAM channels, but SSD, neural engine, I/O and display should all be comparable. I think they just supply the 140W adapter with all 16" models to make their SKU-tracking lives easier... The 14" never comes with the 140W adapter - the M3 and lower-spec M3 Pro come with the 70W adapter, while the high-spec M3 Pro and M3 Max come with the 96W adapter.
Could it be as simple as the cutouts in the box? The 70W and 96W adapters are NOT the same size, so they do need two inserts for the 14" box (but it could be as simple as a small extra insert that makes the hole smaller for the 70W). The 140W adapter is both considerably larger and rectangular, so it would require two entirely different box inserts for the 16" if it sometimes came with the 96W brick and sometimes with the 140W unit. Maybe it's just that simple - the 140W brick is necessary for certain 16" configurations and Apple doesn't want to use different boxes, so they just put it in all of them?