Glad to know RTL is working and no deodexing is necessary.
The developer of the Auto Patcher admits that are still some issues with the application.
Did you try another reader rather than the Stock reader. I find Cool Reader rather superior (Partial refresh, user fonts, style sheet over riding) you can alter anything you want including the fonts, just push the fonts you need to /system/fonts/ and use it in the Cool Reader.
I don't think you'll have problems with Hebrew because as I understand it's letters are not connected.