The hyphenation-penalty setting not being applied is probably the same issue as the custom font - basically I think Plato added some new reader customization options in the span of time since my initial fork, and I didn't catch them to copy them into the reader initialization that's specific to ao3 data. The commandline flag one I will have to dig into a little more to see what it's doing.

Should hopefully have a new build out soonish - I started adding very basic text search (basically the equivalent to using the top searchbar in ao3), so I'll do a new post with that + the bug fixes :)