The options are allow 50-100 saver plus ticket holders on earlier trains if space is available.
That would be extremely difficult to enforce. Effectively you would be saying that saver tickets are valid on earlier trains. Result make aearlier trains even worse.
Limit boarding of the train
Limit the boarding of the train if you can. I am not sure how easy it would be if there are two trains boarding on opposite platforms.
and ignore reservation tickets. If you can't get to the station at time of boarding should the train staff keep a reservation on an overcrowded train? I have been on loads of trains when reserved seats have been empty because people do not turn up.
No that is the last thing to do. Stop on-line sales automatically giving reservations with anything but advance fares unless requested. The problem is people who have already travelled.
I see a possibility for an electronic solution in another age, where the use of (an electronic) ticket on an earlier train would cancel the later reservation.
Add extra train 15 minutes later.
On this occasion that is what they did, but people always want to catch the first train they can.
More practical (perhaps) solutions:
1) Make these trains reservation only.
2) Make the first train (rather than the relief) not stop at Reading as the relief train can cater for these passengers.