PlatinumGames, the developers for both Astral Chain and NieR:Automata, have a history of referencing their other games. There are Bayonetta costumes in The Wonderful 101. There are Nintendo cross-over costumes in the Switch release of Bayonetta. So it is likely to think that Astral Chain references Platinum's last game, NieR:Automata.
The first reference that was spotted, would be at the end of Chapter 3 where Yoseph states the phrase "become as gods". While a biblical reference, this phrase is also heavily tied to NieR:Automata, with it being a memorable phrase in the game, used a few times. and the Xbox One release of NieR:Automata being called the "BECOME AS GODS Edition"
However, this phrase is not the only reference towards NieR:Automata. The other reference in Astral Chain is the role and presentation of a Character, Olive Espinosa. For the majority of the game she is a side character, who has nearly no presense, except as support while you're on the battlefield. Though near the end of the game, Olive becomes a key part of the story, and a chapter requires you to escort her throughout an area. Which sounds awfully similar to a pair of characters from NieR:Automata, Devola and Popola. These two androids are a pair of pinkheaded models that support you through out most of the game, though they can be ignored, then meet you on the battlefield near the end of the game.
Of course, there are obvious differences. Like how in chapter 12, Onion becomes the hub where you select all challange missions avaliable there. The characters are by no regard clones or copies of each other, they're very different characters. Yet these characters fill close to the same role, as the others with a very similar design to boot.