To be clear, this is not a question on why alternate forms exist. Obviously there are a lot of historical reasons behind them. It is also not about why people use rarer alternate forms generally. Often they can convey more subtle meaning, like using 已む instead of 止む or 亘る instead of 渡る.
No, the real question is about why authors choose to use versions of a word which, to the best of my knowledge, are both rare/obscure, and convey no extra meaning, even when there are less obscure ways of writing this. As an example of this, and the specific one that prompted this question, is the usage of 莫迦 instead of 馬鹿. The only difference between the two is that 莫迦 seems rare and comes from the old Sanskrit Buddhism stuff. Maybe one could use that if one of those things was relevant, but in the Tsukihime remake, it is used in a completely irrelevant context (calling the protagonist stupid for saying he would never use his power).
Obviously this was just a recent example for me. Another would be for これ. If one wishes to be fancy and write it as a kanji, 此れ or 之れ are going to be more understood than 是れ, but a quick google search will show that the latter is still used in modern published books, even though, again, as far as I can tell, there is no nuance between any of the three.
