The few non-binary people I know are pretty up front about wanting to be referred to as "they" and / or people in the group refer to them as they for example, "what drink does Sam want?" "They want a beer". So in my experience it has been pretty clear, although I admit it took my poor old brain a while to get used to saying it every time.
I think it is good practice to use "they" if you don't know the gender of a person generally (including gender binary people), as otherwise you could get it wrong. As an example, imagine if you had no idea of the gender of a plus one guest for a dinner party, but were talking as if they were a woman "Joan's friend will be here soon - she will need to take her coat upstairs, I wonder what drink she'll have?" and then Joan's friend arrives and is a (cis for example) man. Everyone would be confused.
My take on the article is that the writer is saying the added disadvantage of this in academic writing is that if the gender (male, female, non-binary or otherwise) of a person is irrelevant to the particular research / journal piece, then mentioning it could be detrimental to people being able to read the work in an unbiased way. For example, if a paper was about say "age people want to have children", if a quote was "I want to have children later in life as I want to have a better career and be able to provide more financial security for them", some people may view this differently depending on whether the interviewee was male or female (for example dismissing it as "old fashioned" if a man said it, or "deluded" if a woman said it), which may detract from the science of what the writer was trying to say. That "they" would also cover a male bodied person who identified as gender fluid (or whatever) would be a bonus, but is not I think the main intention. Excuse any typos / poor spelling btw!