Yes, gksu nautilus works with Unity, at least 11.10 which I presently use.
True, many users only use graphical interfaces and the suggestion of Brother Mike will allow you to use one to manage files as a root user.
Linux is rather peculiar among the OSs in that it does not have a common "All Users" folder, that is, a folder all users can read or write to. In Windows it is /ProgramData and in Mac it is /Library. Ubuntu wants data files in either the /usr/share folder, /opt folder or even others. However, all these are owned by root (like administrator).
If Bible Analyzer installed the modules under the users /home folder, only that user would have access to them. I realize most computers usually only have one user, but when writing a program one has to allow for multiple users.
Bible Analyzer will (should) install for all users. That is, all users can run it regardless who installed it. Each user will have their own configuration files but share the common modules. I don't know of any way the user can choose to install an app for all users or the current. This choice is available for Windows and Mac, but I don't know how to get a DEB file to allow the choice.
Nevertheless, you can still place modules in your /Documents/Bible Analyzer folder and BA should find them.
Concerning the issues you mentioned, I will check them out when I can. I am pretty busy this week, though.
As Mike mentioned, to turn off the pesky TTS voice at start, go to Preferences/Text to Speech and select "No Speech at Start."
Developer, Bible Analyzer
But to him that worketh not, but believeth on him that justifieth the ungodly, his faith is counted for righteousness. (Rom 4:5 AV)