That particular book sounds like it needs a lot of editing of the CSS file. If you don't know about CSS, then it will be outside of your ability to fix, but if you know how it can be fixed. It sounds like they hardcoded in text sizes for certain elements. Some books are more difficult to fix than others. A lot depends on how the book designer used CSS.

As far as a study Bible being difficult to use in a mobile device, yep that is the nature of the beast. Fat fingers don't work like skinny mouse pointers, and many book designers still fail to understand this. Consequently they design their heavily linked books just like they would a web page for navigation on a computer. That doesn't work well on mobile devices. Not much you can do about it except make the text elements bigger.