The app is built on the principle of atomic notes as one of its core concepts. All of the app’s filter, visualisation, PDF and data model features build (and depend) on this. So there likely will be no native support for having a single note per PDF.
That said, I plan to offer options to combine individual notes. Dragging multiple notes into a text editor will already combine them. In addition, I envision that one can export all selected notes to a single file, or preview all selected notes together (e.g. via integration with Marked 2). This could also include transcluded notes. And finally, I’d love to present multiple selected notes together in the app’s editor – similar to Scrivener’s “Scrivenings mode”.
Unfortunately, there’s no publicly available test version yet. Please see my reply here.