If we consider a transformation of a field $\Phi \rightarrow \Phi + \alpha \frac{\partial \Phi}{\partial \alpha}$ which is not a symmetry of a lagrangian then one can show that the Noether current is not conserved but that instead $\partial_{\mu}J^{\mu} = \frac{\partial L}{\partial \alpha}$.
I think the way this is derived is as follows $$\delta S = \int d^4 x \, \delta L = \int d^4 x \left( \left( \frac{\partial L}{\partial \Phi} \delta \Phi - \partial_{\mu} \frac{\partial L}{\partial (\partial_{\mu} \Phi)} \right) \delta \Phi + \partial_{\mu} \left(\frac{\partial L}{\partial (\partial_{\mu} \Phi)} \delta \Phi \right) \right)$$ Then the first term is zero due to the equations of motion and so we are left with the second total divergence term with $$J^{\mu} = \frac{\partial L}{\partial (\partial_{\mu} \Phi)} \frac{\partial \Phi}{\partial \alpha}$$ so we are left with $$\delta S = \int d^4 x \, \alpha \partial_{\mu} J^{\mu}.$$
Writing out $$\delta L = \frac{\partial L}{\partial \Phi}\delta \Phi + \frac{\partial L}{\partial (\partial_{\mu} \Phi)} \delta (\partial_{\mu} \Phi),$$ inserting $\delta \Phi = \alpha \, \partial \Phi/\partial \alpha$ we see that $$\delta L = \alpha \frac{\partial L}{\partial \alpha}.$$ Then we can compare with the above and deduce the result.
My questions are:
What permits the use of the equations of motion here? If the equations of motion hold then $\delta S = 0$ identically in that the solutions to such equations minimise the action. Using the equations of motion gives me $\int \partial_{\mu} J^{\mu} d^4 x = \delta S$ in the end as shown above but since I used the equations of motion isn't this just equal to zero? And also since we are always left with an integral of a total divergence isn't this always zero on the physical assumption that the field variations vanish at infinity/boundary of experiment?
I've seen the nice questions and answers posted e.g here https://physics.stackexchange.com/question/327999/ and the answer here by Qmechanic Which transformations *aren't* symmetries of a Lagrangian?
Basically I'd like to understand what was said in that answer and see it in practice with the above non symmetry of the lagrangian.