Don’t worry about Linux, and don’t try to over complicate things. If you are set on going the Linux route, get a Raspberry Pi. It will give him something really flexible and cheap to experiment with later on.

Look into modded Minecraft. There is a mod called Computer Craft where you can write programs in Lua. One of the things that makes scratch so good for kids is that the results are instantly visible. This is important for kids.

www.curseforge.com/minecraft/mc-mods/cc-tweaked

There are programs to control your reactor > www.youtube.com/watch?v=N9fC3khXuj8

Unmodded Minecraft has Redstone where you can build logic gates.

Outside of what you already have check into a maker space or a computer club at school. Here in Atlanta there is www.codeninjas.com. Maybe there is something similar in your area.