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that is correct. the annotations, highlights etc are stored outside of the book ( that is also how Amazon/Kindle deal with annotations)
readers like Kindle, Moon, Bookari are able to re-display the ebook with their saved annotations , highights etc but that is re-assembled on-the-fly
otherwise the reader has to be able to open the book and amend it's contents., which not many people would approve of.
remember that most android readers are designed for epub/mobi with a bit of pdf support thrown in. and many potable devices lack the horsepower to open up and edit those + there are
no obvious standards for how you would add an annotation to a book so that it made sense also to other readers
have you looked into what adobe can offer, they have a good android pdf reader...and I think it had nagged me to upgrade to some slick proprietary cloud solution... i expect they charge a lot for edit/write to functions though, like on the PC - basic reader is free, everything else costs.
Also, go to google play store & search PDF reader and you will see many apps designed for pdfs. some may have free trials... I went through a lot of those, trying and failing to find one that could read from an index in one pdf and open the linked pdf at the correct page...
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