Our company has used the Product Based Planning component of Prince2 for the past several years and it can work with MS Project, or any scheduling tool quite nicely. However, I will add that we use no formal Prince2 type tools so therefore I can’t comment about any type of automation to get Prince2 data from another tool into MS Project. I can tell you this.
The Product Breakdown Structure (PBS) effectively becomes the project schedule WBS structure. We use a component of MS Office called Smart Art to develop our PBS. Smart Art is comprised of two components; a diagram and an outline format that controls the diagram. Once the diagram is completed, the outline component can be copied into MS Project as the WBS structure. Note that this includes all PBS items including the simple products.
The Product Descriptions help identify the tasks that need to be created for each simple product and help identify needed resource skills.
The final component we use is the Product Flow Diagram (PFD). This is in essence a first cut at the project schedule dependency relationships – but at the simple product level.
I’m leaving a lot out of this answer, but in essence the Product Based Planning component of Prince2 provides a tremendous approach and structure to help the PM and project sponsors identity the project scope, work products, resource skill requirements, and the high-level product dependency sequence.
Hope that helps