This I'll concede. I misinterpreted your point and tone as "don't rely on anything you haven't already measured". I would also agree that it's rather grating to read things that say "X totally happens (according to model Y)". But I don't think that it is inherently bad for one to say "Model Y predicts X".
> No. It started as a model (or idea), but every single step was confirmed using the actual world, and not a model.
This however, I do disagree with. It's still a model. It wasn't "confirmed"; it was "not disproven". Physics will always be a model. I don't see the problem with saying "this model turned out to be wrong so we need to come up with a better one" (exactly what's happening in the article). A large number of important breakthroughs in physics were from scientists demonstrating the failures of models or running into them accidentally (see caloric theory and the Michelson–Morley experiment).