We propose a nonparametric two-sample test statistic for low-rank, conditionally independent edge random graphs whose edge probability matrices have negative eigenvalues and arbitrarily close eigenvalues. Our proposed test statistic involves using the maximum mean discrepancy applied to suitably rotated rows of a graph embedding, where the rotation is estimated using optimal transport. We show that our test statistic, appropriately scaled, is consistent for sufficiently dense graphs, and we study its convergence under different sparsity regimes. In addition, we provide empirical evidence suggesting that our novel alignment procedure can perform better than the naïve alignment in practice, where the naïve alignment assumes an eigengap.