I'm using Baan IVc4, but the situation sounds like it might be similar.
When first inserting a sales order line and entering a generic item on the item field (tdsls041.item) the question "Define product options immediately?" is asked. After saying "Yes", and exiting the product configurator a product variant has been created with the reference option as "Sales Order", and the reference order as the sales order. Now, if a project structure is created for the sales order the reference option will change to "Project", and the reference order as the project. Exactly the same happens for sales quotations and budgets.