We study boundaries arising from limits of ratios of transition probabilities for random walks on relatively hyperbolic groups. We extend, as well as determine significant limitations of, a strategy employed by Woess for computing ratio-limit boundaries for the class of hyperbolic groups. On the one hand we employ results of the second and third authors to adapt this strategy to spectrally non-degenerate random walks, and show that the closure of minimal points in $R$-Martin boundary is the unique smallest invariant subspace in ratio-limit boundary. On the other hand we show that the general strategy can fail when the random walk is spectrally degenerate and adapted on a free product. Using our results, we are able to extend a theorem of the first author beyond the hyperbolic case and establish the existence of a co-universal quotient for Toeplitz C*-algebras arising from random walks which are spectrally non-degenerate on relatively hyperbolic groups. Finally, we exhibit an example of a relatively hyperbolic group carrying two random walks such that the ratio limit boundaries are not equivariantly homeomorphic and no two equivariant quotients of their respective Toeplitz C*-algebras are equivariantly $*$-isomorphic.