It sounds like you're on the right track. Here are some thoughts based on my experience as a kid (early 2000s):
- Find a space for a table. My father cleaned up the pile of scrap lumber in a corner of the basement, accomplishing two things at once (clean part of the basement, give me a layout). Understand this will likely grow.
- Help him brainstorm a permanent track plan, but don't start building it right away. Let him set up and change things on the table. My father and I had planned a L shaped table, but just built one half of it at first so I could start playing around, then once we had the second half actually started on the build.
- Encourage him to do a lot of the research and planning, and then construction (including wiring). OGR, CTT, and other magazines are good for kids, even if above their "reading level". They can also provide a good way of encouraging young readers. (i.e. I want to understand this train thing so I'll push through the difficult reading) The skills I learned building and wiring proved immensely useful as well (both the physical skills and the mental approach).
- A track plan with two isolated loops (perhaps with an insulated crossover) was/is a great solution for allowing the use of remote and conventional control on the same layout. They don't have to be boring either. I mentioned above the L shaped layout, that gave interest in and of itself, and enough space for the outer loop to climb a grade, cross over the inner loop, cross back over, and then descend.
- A newer power source might be a good idea just for peace of mind. (better insulation and more importantly better circuit breakers)
- Understand the layout plan will either be set in stone in his mind, or change daily. Both are ok.