The customer for a coach operator is the traveller. The customer for a rail franchisee is the civil servants at the DfT or other body which grants them the franchise. For subjective things like comfort, your best bet is if the civil servants will actually use the services they're controlling. To that end, it's best for rail operators that don't serve London to be managed by civil servants based outside London. ScotRail has always worked fine because the people in charge work in Glasgow and Edinburgh, while Northern and TPE were controlled by people far away.
The other factor is that coach services don't have to worry about standing passengers. If paying for better seats means that your coach ends up with a full passenger count of 50, then that's excellent. If it means that the coach becomes so popular that 60 people want to travel instead, then you can just price the bottom 10 people off the coach and pocket the increase in fares. Train operators just cannot do that. If 500 people turn up and there are only comfy seats for 450, then 50 people are going to have to stand. If this happens a lot, then these people will complain, and they'll end up pushing for a solution that gives them 500 less comfy seats instead. That's why the new Greater Anglia trains have 2+3 seating. There is too much political demand for a seat to be provided at all, rather than a smaller number of more comfy ones.
Mandatory seating reservations might help, but they're difficult to implement on services which are necessarily overcrowded unless you're happy with lots of standing passengers. Would you want the train with 450 comfy seats to leave 50 people behind, banned from even standing? Coaches and planes don't have to worry about this because they aren't allowed to take standing passengers regardless of how much they might complain about being left behind.