The council will not usually be bothered with boundary disputes unless the boundary dispute, if not resolved in your favour would affect, for example the right-of-way/access and that would adversely affect the development.
If for example the whole plot was 100 feet wide and you are building a house in the middle and the neighbour is now maintaining that the left-hand boundary should be 12 inches further over than it is, it should not affect the application for planning because it doesn’t make a material difference.
If however there is a dispute over whether drive vehicles over that land and that access is required from the highway and there is no other safe access, it would make a difference.
Similarly, if there is a restriction on the land which says that it cannot be built on, that is a matter between the owner of the land and whoever has the benefit of any covenant on it and not the local authority. The local authority can grant planning commission even though there may be a restriction and they can refuse planning permission even though something may be specifically allowed.
Incidentally, the only valid reasons for objecting planning applications are obviously that it breaches any rules or regulations and from the neighbour’s point of view, that it has an acceptable effect on the neighbouring property. A person can’t object quite simply because they don’t like it or don’t want it. It is the effect on the property which is relevant.
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