Hi Ryan,
IIRC one problem with annotations was to get it to synchronize properly. Since annotations are not uniquely identified, I tried to match the bounding boxes but this is tricky, because they might differ in size.
Secondly, the annotation format of KOReader is a bit opaque and not really documented. There even are multiple versions of how something can be done.
Also, annotations for PDFs are stored twice: once in the .sdr folder as metadata and optionally in the PDF file itself.
I definitely think it is possible to integrate and synchronize external annotations into KOReader, but because there is no API for this and because the annotation format is underspecified it would be an unpleasant developer experience and take some time
