Most of the structures can be damaged or is mineable. Those, which is not, is a part of area integrity protection. And if i change it - then players may get advantage by getting acces to resources holded in this areas.
It's all about luck or badluck where new area (and which one) is appear.
You can load previous autosave and hopes what thos area is not appear, or you get another one and/or at on another spot.
This it is question about area design, not about mod restrictions or mechanics.
And if you has an ideas how to improve some area prototypes - share it.