I had a play around. I think you are firmly in toy train set here. I also think a 6 by 4 board will be heavy (it needs to be portable I understand). This combined with the small size would preclude any thought of gradients and multiple levels. With that in mind here is a suggestion.
It allows a 3 carriage loco hauled train or four car DMU/EMU/HST that would have to reside on the running lines. Three sections on the roundy-roundy allows you to swap trains between the lines. Your son can blast around the outer loop whilst you shunt about on the inner. It has an inglenook shunting layout on a goods served industry, a TMD and carriage sidings. Industrial buildings and a polystyrene hill and road bridge provide a scenic break between the two sides without great additional weight. The buildings could be removable to aid storage, ditto the trees. They could be inserted into the polystyrene to reduce the height of the final board when stored. The points are a combination of set track and stream line. You will need set track spacing for the curves anyway. The station is an island platform with the rest having to be imagined off scene.