A major difference is that The Matrix has a base reality that is obviously the true reality, while eXistenZ does the impossible and makes us accept the most bizarre reality ever as true. And oh what a reality it is. Maybe it s because of how the mundane is mixed with the bizarre. Technology is organic, but only some of it. Cars are normal.
Gas stations are the same.
Cell phones are glowing bug like appendages. High technology has been replaced with organic creatures, and it provides a truly surreal setting for the characters. Unfortunately he is lacking a fundamental requirement for playing, a bioport. But the plot, while cohesive in it s own creepy way is secondary to just trying to figure out what the hell is going on in this universe. Cronenberg just slaps this weird organic-tech world into the viewers lap, and it s up to you to figure out how all these things work.