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To clarify your requirements: there is a big difference between PDF annotation that you might do with Acrobat Reader, FoxIt, PDF Expert etc., and annotation you might do with a reading device.
The former are saved with the PDF, the latter are not.
Reading apps treat the PDF as 'read only' (ReMarkable is somewhere in between: I guess you can add delete and reorder pages, don't know how it handles annotations: are they real PDF annotations that Acrobat Reader interoperates with?).
Generally you export a list of highlighted phrases and any associated notes, but they are not 'merged with the PDF'.
Scribe will export a flattened PDF with pen annotations and highlights on an image layer. Text notes are not represented. That might be useful if you are using that to make updates to some original document and all of your markup is in form of handwritten notes and highlights.
It will also export a PDF list of 'Notes and Highlights' similar to what you would have for regular books. This will have large page thumbnail images with handwritten notes for each page with handwritten notes, plus highlighted phrases and text notes in the order in which they occur, each with page number references.
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