Go back and check what they need. I presume this is registration for rates. The construction stage you are at will have been flagged up to LPS by BC during the course of their inspections - normally 6 months before the anticipated completion of the works - but I doubt you have to be complete for a certain dates.
Post the plans and the other existing and proposed elevations.
The only reason I can see for the request for a flat roof is to distinguish the existing from the proposed - a bit of a shit request really and as for the window why on earth are they getting their knickers in a twist about a single existing window - madness.
Tell your neighbour to move his soil away from your building and into his own property.
I can see a situation where your neighbour extends their garden the 100mm into your property and up against your extension so that over time the extension wall becomes the boundary. Nip this on the bud now.
Dig foundations into virgin ground.
Build up sub-floor blockwork to height you want.
Fill inside and outside with good clean fill well compacted.
Form precast or reinforced sub-floor.