Schwinger-Dyson Equations (SDEs) can be understood in a myriad of different ways. In the Canonical formalism, they come from the non-commutation between time differentiation and the canonical time ordering (as opposed to covariant time-ordering in the path integral formalism). But in the Path Integral Formalism, there are two ways, at least that I'm aware of, to obtain them:
The first, is to integrate by parts, that is, given some functional of the field (we'll assume one scalar for simplicity) $F[\phi]$ $$ \frac{1}{Z[0]} \int\mathcal{D}\phi \frac{\delta F}{\delta{\phi}}e^{iS[\phi]}=\frac{1}{Z[0]} \int\mathcal{D}\phi\frac{\delta}{\delta{\phi}}\left(F[\phi]e^{iS[\phi]}\right)-\frac{i}{Z[0]}\int\mathcal{D}\phi\left(F[\phi]\frac{\delta S}{\delta{\phi}}\right)e^{iS[\phi]} $$
where $Z[0]$ is just the normalizing vacuum to vacuum amplitude. Then, assuming there are no non-trivial boundary conditions, the total functional derivative vanishes and we find the SDEs $$ \left\langle\frac{\delta F}{\delta{\phi}}\right\rangle=-i\left\langle F[\phi]\frac{\delta S}{\delta{\phi}}\right\rangle $$
where $\langle ...\rangle$ is shorthand for vacuum (covariantly) time-ordered expectation value.
Whereas the second method relies on redefining the field. That is, given $$ \frac{1}{Z[0]}\int\mathcal{D}\phi\, F[\phi]e^{iS[\phi]}. $$
One can take $$\phi(x)\to\phi(x)+\epsilon\, \eta(x),$$ and expand the path integral to first order in $\epsilon$. What one will find is that the zeroth order term saturates the equality, leaving us only with the first order term in the expansion $$ \epsilon\int d^4 x\,\eta (x)\left[\left(\frac{1}{Z[0]}\int \mathcal{D}\phi\frac{\delta F}{\delta \phi(x)}e^{iS[\phi]}\right) +i\left(\frac{1}{Z[0]}\int\mathcal{D}\phi \frac{\delta S}{\delta \phi(x)} e^{iS[\phi]}\right)\right]=0. $$
And because this should vanish for any choice of $\eta(x)$, the integrand must vanish identically, leading us to the SDEs again.
My question is about the assumptions necessary for these to hold. In particular, the first one requires trivial boundary conditions, whereas the second appears to not require this at all. I have no issue with the fact that in canonical quantization the SDEs come from an entirely different place, after all, the formalism is inherently different, but things should be consistent given a formalism. Maybe the trivial boundary condition requirement is hidden somewhere in the second method and I'm just not seeing it?