They were still catching up from the delays at about 17:00 at Southampton. Imagine what it will be like on GWR▸ when Paddington is running at capacity.
Stepping aside from the particular (trespass) incident to the more general case, as you are doing, one does wonder how much planning is based on an "everything is right" scenario. One in which no trains are broken down, there are enough staff for operational duties, the axle counter at Thingley is working, the weather is neither too hot nor too cold, passengers are not being taken ill on trains, and no-one who shouldn't be is on the tracks for any reason. One in which the signals are working, the knitting is properly in place, and no pigeons are exploding to bring down key stones in bridges.
Problem is ... even if each of the things I have mentioned is a rare abnormality, they compound to make a situation where there's always likely to be something wrong somewhere in the franchise. And that's where good recovery plans come into place.
I would suggest if the every-30-minute Oxford or Bristol service from Paddington is over 15 minutes late, it might be better to can the following one rather that have a knock on for many hours. Thinking back to recent time trains graphs (but I don't have a copy with me today) it's amazing how long it takes for a problem to drop out of the system and occasionally being "cruel" to people for half an hour is being kind to everyone looking to travel for the following 3 or 4 hours. Buses already "drop back" in this way, and I think they do it on the tube too.