PDF.js recently added a support for saving AcroForms annotations, and this serves as a very good example how to implement a basic append based PDF writing.
Append based writing fits probably better in our case as it's less invasive on PDF structure especially because annotations writing/deleting/modifying is relatively basic operation.
Therefore PDF Assembler becomes a useless intermediary that has to be maintained and reduces performance for this specific annotations-related use case. It also doesn't support encryption.