I think a way to make these puzzles a little less potentialy frustrating would be to make rooms interact in some ways, and a solution for a puzzle would be to arrange them in a certain way. An npc could hint that the entrance to water town is behind a waterfall, and to make a waterfall you would have to put a river room next to a mountain room and it would create a new waterfall room in an adjacent unexplored tile.
I think it would then be fun for a player to experiment with different room combinations without any destination in mind, just to see what unique rooms they can make. Maybe the player tries surrounding a dessert room with water and it creates a little tropical island. Then these unique rooms could have clues for the more harder puzzles, which would be more convoluted so a player doesnt just stumble into them by accident.
Maybe new rooms could also change old rooms, so for example if a careless player put a river room next to a valley room, it would flood it and prevent the player from traversing it normally.
Also I think the GROW games are an example of a puzzle where the challenge is to guess a specific sequence of choices using clues and some trial and error, which I feel is sort of like the puzzles you described.
I feel like getting very specific sugestions could be annoying, especially when you have narrative themes already in mind and have to marry them with the mechanics, or maybe you already though of this and decided its not the right solution, so feel free to ignore me and my ideas and ban me from ever buying any Melos Han Tani game forever if you feel that way.