It has to do with simplicity of story and language, too. Chapter books are fairly linear, where MG books can have more twists to explore the world.
A problem in a chapter book is something that could be explored in an episode of a kid's cartoon. Something like the Magic School Bus. A regular MG novel would be more like a season's arc of a show. There are more complex characters and side plots that may or may not tie into the book's plot.
The first Junie book was less than 7,000 words and it was about Junie learning not to hate riding the bus. Junie was 5 years old and spoke like a baby. She has a series of books, but they're not really connected to the point that you couldn't read only one in any order.
The first Percy book was over 80,000 words and it was about Percy coming to terms with being a demi-god, saving his mom, making friends and enemies, locating a lost thunderbolt, uncovering a plot by another boy at his demi-god camp, and setting up the entire Percy series that would come after.