Consider a complex scalar field with Lagrangian $$\mathcal{L} = (\partial_{\mu} \bar{\phi})(\partial^{\mu} \phi) - V(\phi)$$ with potential $$V(\phi) = \frac{1}{4}\lambda(\bar{\phi}\phi - \eta^2)^2$$ The model is invariant under global $U(1)$ phase transformations. The minima of the potential lie on the circle $|\phi| = \eta$, and so the vacuum is characterized by a non-zero expectation value: $$\langle 0|\phi|0\rangle = \eta e^{i\theta}.$$
Now, here is where my confusion lies. The $U(1)$ phase transformation would change the phase of the ground state into $\theta + \alpha$ for some constant $\alpha$. If the symmetry were still manifest, then we would not have found this and instead returned to $\theta$ alone; therefore, the symmetry is broken. However, the broken symmetry vacua with different values of $\theta$ are all equivalent. So, what would it matter if considered $\theta + \alpha$ as opposed to $\theta$ as surely the two represent equivalent vacua? If this is the case, then why is the phase transformation not a symmetry of the vacuum, if it works only to move me to an equivalent configuration? What am I missing?