microsoft edge browser now supports annotating epub,within the file, and there is a version of edge for android( but dunno if the android version has this new feature.
https://www.howto-connect.com/annota...er-windows-10/
Moon reader only
reads the epub ( as do most readers). annotations are written to a separate file.
I am not aware of any epub reader app that actully changes the source book file, nor of any standard for how/where such changes need to be made , so that book is still a valid epub