Chiming in here. These are all perfectly valid points. What I do think you're missing though is the fact that most passenger who experience overcrowding or chaos as a result of no guaranteed seats, are not being presented the question "would you rather have a low-flexibility, high-cost railway, that's a bit more comfortable or one where most people can actually travel if they want to, it just may be very busy at times?"
The questions that are presented are a lot more simplistic at that, and all fail to mention that a move towards a more 'comfortable' railway requires either an increase in investment, or pricing even more people off the trains. Certainly if I asked the people sitting on the floor of the morning peak King's Lynn - King's Cross train, "what would you do to fix this" they'd say "add more carriages", because that's an actually sensible solution. Pricing people off to make it nicer for others is an extreme version of robbing Peter to pay Paul, where in this case Peter is on a modest income while Paul can afford to take a high-demand train service post-price hike. I think the priorities are just in the wrong place.
In the KLN-KGX example, a lot of morning peak trains are already over double the cost of the off-peak fare for lots of people - having to pay the anytime fare + railcards not being valid that early, results in around a 60% price rise. If you want to eliminate overcrowding on this service, you'd likely have to do another 60% price rise. For those paying £60 for a peak time train ticket that's also overcrowded, the current system feels unfair. What's even less fair though, is charging £80-100 with everyone else switching to driving.
Add to that the fact that making a few dozen exceptions or additions to what's otherwise planned to be a fully French-style ticketing system, is just adding more complexity. Having people on TfGM-set fares taking an intercity operator between Wigan and Warrington, or busy peak-time trains that form commuter services (e.g. into Reading, Coventry or Wolverhampton) somehow barring short-distance travellers, are all strategies that add to the complexity of rail ticketing, they don't reduce it. When you consider that this plan would anyway result in loss of flexibility and price-hikes, I'm not a fan of that trade-off.