Such a choice is a matter of tone and style. I'm not sure that I would ever agree that it could be "not justified" as there is always at least a subtle difference in rhythm and flow, and often in meaning. Intentionally choosing or avoiding words with latinate roots, for instance, can be valid style choices. Intentionally choosing a less well-known term can affect style, possibly giving an academic air, or a more everyday feel to a piece of prose. Also, a word's history, via its etymology, can influence how it will affect knowledgeable readers.
So I might describe such a choice as "using a more intricate style" or "a more complex style". Style should suit purpose, of course. If the intended audience will not be likely to get a nuance, and may well misunderstand a word, that was a stylistically poor choice. If the intended effect will not be enhanced by a particular choice, that is also poor style.