Whoa, weird! I've replicated the relevant parts of the layout based on that minimap screenshot, and the rooms connect as expected for me. There shouldn't be anything extra required, so I wonder if something subtle is causing a logic bug somewhere. Could you send me the world file? If you don't have an easy place to host it, feel free to upload it using this world submission form (if you put your username here as the e-mail address, I'll know it's in reference to this thread; the process isn't automated, so the world won't actually get published right away): https://ludobloom.com/leafsodyssey_worldupload.html
Aha, I see it now - I didn't notice in the minimap screenshot, but there's actually a column of pit tiles in the room at (-1, 0, -1) between the two rooms. Subtle enough not to notice, but it's separating the two by a tile. Just gotta shift everything over to the right a bit and the two rooms should connect properly!