Well, it's a little ambiguous what it means for something to be "physical". Certainly an outcome that can be verified using any frame is physically meaningful. But the reasoning used to explain/predict the outcome is often frame-dependent. Different frames would explain the same result in different ways. But being a little more loose, you could consider frame-dependent (or more generally, coordinate-dependent) effects to be "physical" if they can reliably be used in predicting physical effects.
The difficulty in reasoning about thought experiments such as Bell's spaceships, or the barn and pole, or the twin paradox, or whatever is that we don't actually have any Lorentz-invariant equations of motion to apply. If we did, there would be no ambiguity: Just pick a frame, and apply the equations of motion. If the equations are Lorentz-invariant, then you get the same result, no matter what frame you pick. But if someone just tells you "I have a pole moving at close to the speed of light" or "I have a clock moving at close to the speed of light" or "I have a string connecting two rockets moving at a significant fraction of the speed of light", you don't have equations of motion to derive the result. Instead, you have to use rules of thumb and intuition about how poles, clocks, strings work. The rules of thumb that we are most comfortable with are Newtonian physics, which are only applicable when things are moving slowly relative to the speed of light. So you can try to analyze things locally, in a frame where things locally are moving non-relativistically, and hopefully piece together the local pictures into a global picture.
But Bell's argument with his spaceship paradox is that we can augment purely Newtonian reasoning with intuitions specially developed for SR. He claims that we should start to think of Lorentz contraction as a physical thing, to get an intuition about things moving relativistically. The rule of thumb is: If you take an extended object, and accelerate it to relativistic speed, then it will tend to contract. To prevent it from contracting requires applying stresses on the object. Whether you call such reasoning "physical" or not is a matter of definitions, but Bell's point was that, at least in many circumstances, such reasoning gives you a quick intuition about what the right answer is.
I don't think that the ladder/pole paradox contradicts Bell's contractionistic reasoning. From the point of view of the barn frame, the pole is contracted, and it is possible to close both doors simultaneously. And if the barn doors are really strong, compared to the pole, it IS possible to get the entire pole into the barn at once. Of course, using "contractionistic" reasoning, you would conclude that AFTER the barn doors are closed, the pole would expand to its normal length, and would get smashed to pieces by the strong barn doors.
You get the same conclusion from the point of view of the pole. From that point of view, it's the barn that is contracted, not the pole. But it's STILL possible to fit the pole into the barn: You smash the barn into the pole at relativistic speed, and the pole will be crushed to a size that fits inside the barn.