"In my experience loft space belongs to the freeholder of the property, now as you would be having a shared freehold the loft space would not automatically belong to the upstairs flat although that sounds counterintuitive."
This is what I've always been led to believe and you, as part freeholder, would have to give your permission at the least or sell your share. Also, I believe in the cases of roof extensions to flats, planning permission has to be obtained even if what is proposed is within permitted development. Are you getting new leases drawn up with the purchase of the freehold or will the existing ones carry over? I think, for your peace of mind, you need to consult a solicitor.