Graphs are invariant under node permutations, motivating permutation-equivariant architectures in generative models. In flow matching, however, symmetry also affects the source-target coupling: one must choose both which graphs to pair and which node representatives to align. We study these two forms of alignment, termed outer and inner alignment, and their effect on equivariant graph flow matching. We connect inner alignment to transport on the graph quotient space, whose Euclidean quotient metric coincides with Gromov-Monge distance, and show that quotient couplings admit aligned representative lifts while symmetrization yields equivariant flow-matching minimizers, including for categorical endpoints. In practice, we compare random augmentation, permutation-blind minibatch optimal transport, approximate Gromov-Wasserstein alignment, and combinations of inner and outer alignment. Across continuous graph and molecular generation, alignment can substantially simplify trajectories and improve few-step generation, while its benefits depend on the alignment and computational budget. Our results highlight that effective graph flow matching benefits from alignment both inside and across graph pairs.