It is easier than ever to read epubs on neat-reader.com with the vocabtracker extension.
This tampermonkey script which will autoremove furigana (and okurigana) and make vocabtracker work as normal (I am still in a dialogue with vocabtracker to figure out a way to include this to the chrome extension):
https://greasyfork.org/en/scripts/470976-remove-furigana-neat-reader
Published a new script that modifies the furigana instead of deleting them. It is still a bit buggy for some verbs but talking to vocabtracker about it. https://greasyfork.org/en/scripts/470975-change-furigana-neat-reader
it should be noted that this messes up with some books like 京極夏彦s 百物語 so make sure and check that only furigana is removed if the text looks like nonsense