Well, there's playing with the medium in the meta sense, and then there's going too far with it. Nagito's "game" had a rather reasonable reflection on reality, and while DR2 takes place in a virtual world, there's a lot of foreshadowing to that - and despite being inside a virtual world, the events do actually take place and affect the characters - which also reflects on reality.
Meanwhile, going "haha, just a prank, none of it happened, all of it is just anime made by that one anime dude" would have no point to it. From a storytelling perspective, there's nothing to gain from voiding everything that happened. So that's kind of unlike the examples of DR2 or DR:AE. Having some meta elements doesn't immediately mean any and all meta you could ever come up with is something that could actually happen.