Clearly, the screws were too long and the cills were fixed from the underside.
The remedial "solution" proposed is an easy bodge and I think you realise this.
Whilst it is merely an aesthetic defect, it is nevertheless unacceptable and was fully preventable. Ask yourself if you would accept this in a new car?
So what can and should be done.
The window should be removed and the correct length screws fitted to the underside of the cill. Following re fitting, the surface holes that are left should be filled and cosmetically repaired by a "plastic surgeon".
Please remember Crest made a 20% profit on your home, they can well afford to give you the standard of new home you were expecting.