You are concern in this regard is justified and is natural especially foreseeing the future issues.
The act of sealing the gutter is against the law, the builder cannot take law into his hand to seal the gutter and utilize the same for some other purpose as mentioned by you.
The builder may depart from the scene after having sold the entire flats, leaving the flat owners to face the problems in this regard especially over such illegal structures.
The approval of BDA does not means that the builder has been authorised to seal the Nala, have you confirmed this from the approval granted by BDA.
There is no point in builder leaving space towards buffer zone when he has totally sealed the entire buffer zone by a concrete cover,
You may better obtain a proper legal opinion particularly insisting your concern from a local lawyer and proceed only if recommended.