The fallacy here is the idea that there are general rules at all. There are no general rules about what is allowed in an academic paper, or any other kind of writing. There are specific style guides -- some public, some specific to a particular institution or publication -- and their rules cover the particular institution or publication that publishes or ascribes to them.
So, the only requirements that you should worry about are those imposed by the particular publication or institution you are writing for, and those rules should be contained in a particular style guide.
If two style guides differ on some rule, this is not a disagreement, it is merely a difference. If two soldiers from different armies exchanged clothes, then both their respective commanders would consider them to be out of uniform. But if they met a soldier of a different army in the uniform of that army, they would not consider them to be out of uniform, even though the uniform they were wearing was different from their own.