A printed document in your hands is better than a computer document on a screen, even though having both is better than having just one. This goes for Bibles and for Bible studies. That's why after you use the Studies tool to write a Bible study you use the Generate tool to create PDF files of it. PDFs are the best way to store a document on a computer if you intend to print it. This emphasis on printing is also why on the backend PDFs are generated using a desktop publishing program. Desktop publishing is the best way to control the appearance of each page of a document.
If you want total control you can actually install the backend's desktop publishing program on your computer and use it to manually tweak a document, using the document's so-called SLA file. Using the SLA file is discussed in the help on the main Bible page and on the main Study page. Just know that desktop publishing is an advanced computer skill. It's basically word processing on steroids for control freaks. Resort to it only if you have to.
So, document generation gives you the benefit of desktop publishing for your studies and customized Bibles. As time goes on more features will be added so that you can get the document you want without learning desktop publishing, and also do more with those documents. Below are some areas where improvements are being planned or at least considered.
Fonts
Marginal Notes
Books
Distribution