I’m not sure what you’re using it for, but I use an ebook reader called eBoox. It’s free with no ads, not sure if open-source. I had bookmarks but I don’t think annotations. I like it because it can open my epub, mobi, and pdf books, change the font and font size, sepia and night modes, has many options for how to change the page, and fairly simple UI. The creator markets it as a cutesy cat thing, but that is only present on the initial setup and then it’s just a regular e-reader app.

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The built-in Books app can do bookmarks. I just tested to confirm. It can import PDFs.