General style issues pertaining to biblical and theological studies have to do with things like punctuation, numbers, terminology, and transliterations. Regarding punctuation, should you use an apostrophe s or just an apostrophe with a noun that ends with an s (for example, Jesus' or Jesus's)? Or what is the proper way to refer to a biblical verse: Rom 1.16 or Rom 1:16? Regarding numbers, when do you spell out a number or not? Regarding terminology, often specialized disciplines have many terms that are perhaps spelled a certain way or have a specialized meaning (for example, what's the difference between lowercase gospel and capitalized Gospel?). And with regard to transliterations, characters in languages that do not use a Latin script (e.g., Hebrew, Arabic, Greek, etc.) are given standard Latin characters for consistent representation where a word processor does not use non-Latin characters.
These general issues are discussed at length in §4 and §5 (pages 12-67) of SBLHS.