Didn't plenty of new ideas start with analogies? I can think of Feynman and Einstein who described imagining or noticing things in real life which gave rise new ideas in physics.
You would have to explain to some extent what the analogy is, and what it means for the real world, before we could begin to discuss whether it is in any way correct, let alone useful.
Probably just a semantic difference in what they mean by "start." In this instance, the waterbed analogy would suggest some sort of negative mass-energy and a mass-energy conservation law.
Just to be clear- are you implying that people cannot be inspired by natural events and think of an analogy elsewhere in physics? Or are you saying that an analogy cannot be the firmament of a new theory?
I would agree with the latter, but it sounds like you're stating the former, which is categorically incorrect