Actually existing canon has portrayed the Matrix as being a cross between heaven and Nirvana in a paradoxical kind of way. It's like Nirvana in that all Sparks are destined to return to it (thus it is the place where "all are one") yet it's also like heaven because Sparks still retain their individual aspects even after returning to it.

The Matrix in the movie-universe is a different MacGuffin, so who knows how it works.