So after playing for a bit, I couldn't help feeling that this idea was always at the back of my mind. For a yard filled with hidden bases and places where shrunken people and robots worked, a garden railway off in the corner would be a good way to hide such places, in plain sight. Small model people would be either player sized or even bigger than them, scattered around the village and give the world some more larger than life experiences.
This could also give the game some unique gameplay variants and unique resources to that area as you could find doll house items, and plastic string, allowing new items to be created and stronger barricades. There could also be puzzles related to going around the "miniature" villages, looking for clues and switches to open the hidden base there. Then there is the garden railroad itself, it could be both a threat and a challenging reward, unlock the base to be able to control the trains, allowing players to have a way to move resources and themselves around the layout/environment. To add some challenge, before unlocking the base the trains could run around the layout automated, and can hit players if they aren't careful.
This type of environment would also allow for some unique, weird perspectives of normal items like bridges, buildings, and tunnels, surrounded by grass, giant flowers, and bushes, and potentiality for a new smaller pond with small fish and new hazards like electrified rails and cables. There could even be a small "mountain" with various balancing puzzles as your team works their way up to another lab hidden in a model ski lodge on top. It would allow for a view of the entire environment, the town below, and yard beyond, with hazards like rapids and waterfalls to cross as you climb up.
Overall, I think this game is able to go a lot of fun and unique directions. This suggested environment could entertaining to explore and unlike anything we have seen yet, offering new challenges to both the players and developers.