Thanks for raising the possible concern with R53. Because of this, I reached out to AWS Support and they confirmed if you have this extension and want to use it

Thanks for raising the possible concern with R53. Because of this, I reached out to AWS Support and they confirmed if you have this extension and want to use it with an AWS offering, you can use any domain extension you'd like, even a crazy obscure one (like .ycomb). But you can't buy and host this domain extension at R53 currently.