As the name of the option implies, you get a page per layer. To do otherwise would require Gimp to have an option in the PDF export dialog (or be able to read your mind) to know the group level from which everything becomes really a single output page.
In practice I have an old script that does this: flatten-groups-0.0.py
In practice I have an old script that does this: flatten-groups-0.0.py
- once installed it can be reached by Image ➤ Flatten groups
- you give the level from which everything is flattened
- possibly execute after Image ➤ Duplicate