Concerning the bug that the Castle Planner charges you the entire material costs including the already built fortifications when you try just to add something little like one tower. Once I noticed that after such second-stage addition I had lots of leftovers of construction materials, piled up in the territory of the fortified area. Maybe, the bug indicates wrong quantities of materials required, and won't allow you to start building your addition until you accumulate those numbers, but it doesn't actually use all of them. Like people bring and pile all those materials to the construction site, but actually they use only what is needed to build your little addition. Unfortunately, I didn't count and calculate the exact numbers, but it seemed like that.
You don't even have to build walls to create that "dead blocked zone of the manor". Any separate fortification buildings become points of the perimeter of such zone. For example, build a Manor House, a Garrison Tower and a fortification tower without any walls. The 3 structures will form a triangular blocked zone.