Check out this interesting (somewhat recently GPLv3 re-licensed) game Blackvoxel:
As you can see it has some interesting mechanic which they call "Molecular Voxel Interaction Engine". As seen in the trailer above, it basically allows you to automate crafting, resulting in interesting "programmable" factory setups.
Of course this might sound a bit too much like actual work and not fun... but given the big fan scene for the closed source game Factorio, I would say it can be more fun that it looks at first ;)
Blackvoxel itself probably needs to be a bit more of a game instead of "just" a sandbox, but there is big promise in the overall concept, so give it a try :)
Free, libre games and development news