This guy breaks down just how bad the layout of the new PHB is. The cross referencing is non-existent and the subsections seem to go in the order someone thought of them. I'm sadly unsurprised that they've not improved on any of these problems which existed in the original 5e PHB.
Here's the secret: the book doesn't make them nearly as much money as a first party VTT/subscription service.
All this content is going to be hyperlinked on D&D Beyond anyway, why spend money to improve it? Hell, making it too accessible might even cost them subscribers.