Unwarranted speculation and generalizations purely for the entertainment of those who enjoy a good mind boggle. You'd be wasting your time if you expected to gain any solid insight from the article.
Space and time are what keep everything from happening at the same time in the same place. The infinitesimal bundles of energy that make up objective reality are vastly separated in spacetime. Why is that?
The goo analogy makes it seem like "ripples" and "bends" are something space does, where as it's (from my understanding) actually the influence of gravitational fields/aggregations of mass.
So far it seems to me that they sometimes provide an oversimplified analogy which they revise in a later chapter.
Welcome to every high-school, undergrad and postgrad physics course. That's just how most sciences are taught. Physics especially, because all analogies lead to misunderstandings because they are an attempt to simplify the mathematics underlying the physics[1]. Such analogies will always result in certain subtleties being lost on the student, but if the student is not familiar with the subject then the mathematics would also be lost on them.
The reason why this method works is that physics operates on approximations, so an approximately accurate analogy is a step in the right direction for a more accurate mathematical model (which is still ultimately an approximation).
Part of me knows that a lot of this is being simplified down for me, but I also trust the authors to not steer the reader too far off course.
I may not have all the math and physics understanding, but I get that dark matter is real. I didn't before. That's the kind of thing the book is about, imho.
A one-way measurement of the speed of light is needed to differentiate between the two theories, and that has not been accomplished. In fact, it may not be possible in principle to do so. Choice then becomes a matter of taste and philosophical/physical economy.