Interesting theory, but I think it's more to do with a studio producing work that's in the same vein, towards the same audience and using the hooks that people expect from a pixar film.
The little cross-overs, I don't see those as tie-ins to a bigger universe, more that they are fun little nods to their other works.
The author claims that A Bug's Life is occuring in the post-apocalyptic world, but he doesn't mention the Bug's Life toys which appear in the Toy Story films. He's missing out parts to put his theory together
I must admit that I do quite like those little nods. One of my favourite shows, Firefly, get's a lot of little nods in other programs. It gets a lot in Castle (usually not too subtle and tied in with it having the same main character), but there are some other sneaky wee ones, like the ship from Firefly appearing in the background of Battlestar Galactica. It doesn't mean they are in the same universe, just a little easter egg, a little nod