Haha, I thought someone might say something like that, here is my rational, accept it if you want:
First of all, we have to realize that fc, no matter how realistic parts of it are, is not completely realistic, but let's get back to the topic at hand.
In life we have two types of changes. Those are physical and chemical changes. A physical change can be (at least in theory) reversed to get the same object back. So, for example, bending a piece of paper. In practice, undoing a crease is virtually impossible, but the idea is is that it theoretically can be unbent into the same piece of paper. Nothing chemically is changed, it is the same piece of paper, only STATE has changed.
Now let's consider chemical changes. Cooking an egg, for example, is a chemical change, and results in a different substance than before. (It's easier to see when burning gasoline, another chemical change, where the gasoline turns into carbon dioxide and water, which are completely different substances). It is considerably harder to "uncook" an egg than to unfold paper, maybe even impossible as a matter of fact. This is a more RADICAL change than a physical change.
Now, let's go back to Fantastic Contraption. Phasing is like a physical change. you can phase something through something else, and then you can phase it back. More importantly is is the same contraption, just in a different STATE.
However, joint snapping is like a chemical change. Once a joint is snapped it cannot be unsnapped, and the contraption is now a different one. This is a more RADICAL change, and therefore, at least to me, is a worse form of glitch. I get it, in real life it doesn't work like that, but in FC, phasing doesn't really change the contraption, but joints breaking does.
I understand your rational, but this is mine.