Have you tried sideloading another font to see if you have the same problem?
just from looking at the images, it looks like Bookerly doesn't support those characters and that is why you are seeing the tofu blocks. Does Bookerly give you any issues when rendering those same characters inside of a book? (I think you said it does, just making sure.)
As an experiment, try downloading Google's Noto font. Scroll down to find your language, load it up and see if the problem is corrected:
https://www.google.com/get/noto/ At least then you will know if the problem is sideloaded fonts or Bookerly specifically.