and I guess you cannot turn that part off? Problem is that things you want to delete are not built or placed in the matter of blueprints in the direction aligned with the grid. So if you have a building that has inbuilt items you want to delete then you have to do it piecemeal. This is true long after you lose the ability to undo a blueprint.
Nope can't do it, tied to the grid.
And yeah I've had many cases like what you described. Actually had to deal with one earlier when trying to redo my meditation / tea house down at my lake....ended up just blueprinting the whole thing so I can work on it somewhere else because it's off grid rotated.