To what extent should I follow "style rules" in academic writing?
Your writing should strive for maximal clarity in conveying your intended meaning to the reader -- that is the ultimate goal that overrides all other considerations. Style manuals are simply sets of rules that people came up with that aid writers to achieve that ultimate goal. To the extent that I would perceive a particular style rule on a particular occasion to be in conflict with the goal of conveying meaning effectively and concisely, I would see myself as free to ignore the rule.

The upshot is that as long as it doesn't happen too frequently, ignoring style rules is fine if you do it not out of laziness but out of a sincere desire to make the writing as clear as possible. If you do find yourself wanting to break the rules very frequently, you may want to consider the possibility that your intuition about what makes for clear writing is not yet sufficiently well-developed for you to make the best judgment calls on such things. In that case I would try to stick with the rules until you gain more experience.