Generally speaking, in fiberglass boats, most bulkheads are not structural, especially with respect to the mast loads. If the boat has compression post under the mast, then the deck doesn't actually carry the load. In fact it is trouble when the compression post doesn't carry the load, and the deck does. This often happens when the compression post is wood and the bottom rots out. Or when the post is aluminum or stainless, but sits on a wood block that rots out.
On your boat, if the chainplates are attached to the bulkheads which were cut away, then the concern would be about how the bulkheads are attached to the hull, not the deck, in most cases. Decks are usually installed after the interior is in, so the builder really doesn't want to glass the bulkhead to the deck at that point.
Hope this helps,
Gary H. Lucas