Seats with internal flanges are made from multi-piece moulds. The reverse (internal) lip part is bolted on to the main part of the mould, the moulding is laid up inside the mould. Once cured, the lip part of the mould is unbolted and the moulding can be withdrawn.
The Ballistic (and most other boats with a moulded deck) hull and deck are separate mouldings.
The hull moulding incorporates the hull surface and the outer part of the transom, internal stiffeners and the majority of the transom stiffening.
The deck moulding incorporates the deck surface and the inside of the transom.
The two are sandwiched together. There will be a join along the top and edges of the transom. Along the top this will be either faired and polished with gelcoat and/or mat, around the edges it will be hidden by the tube connections.