Probably you've right.
For others I've made a short tutorial.
1. I defined the boundary of the field (black walls) and the boundary of the river with two tributaries.
2. I've generate the fields (rooms) around the river
3. Delete the field boundary but keep (or enclose the river)
4. Use AutoDimensioning plugin to generate build area.
Go to the newly created level and set a blue color to this area.
5. Back to first level and use Select/Hide Utility plugin to select all walls.
Now you could delete them.
6. Go to Dim level, select the river and CUT
7. Go to the first level and PASTE.
You will have all rooms on the same level WITHOUT gaps.
Now you could delete the Dim level (it is empty anyway)
8. Use Select/Hide to select all rooms and run Terrain generator.
Hope will be useful for someone.