Haven't come across this before, but in case it helps S1(3) of the GPDO 1995 states that: "Unless the context otherwise requires, any reference in this Order to the height of a building or of plant or machinery shall be construed as a reference to its height when measured from ground level; and for the purposes of this paragraph “ground level” means the level of the surface of the ground immediately adjacent to the building or plant or machinery in question or, where the level of the surface of the ground on which it is situated or is to be situated is not uniform, the level of the highest part of the surface of the ground adjacent to it." I suppose this context (i.e. the existence of a basement) could 'otherwise require', but the impact is likely to be no different so not sure why an LPA would make an issue of it.
