Unbalanced optimal transport (UOT) provides a flexible way to match or compare nonnegative finite Radon measures. However, UOT requires a predefined ground transport cost, which may misrepresent the data's underlying geometry. Choosing such a cost is particularly challenging when datasets live in heterogeneous spaces, often motivating practitioners to adopt Gromov-Wasserstein formulations. To address this challenge, we introduce cost-regularized unbalanced optimal transport (CR-UOT), a framework that allows the ground cost to vary while allowing mass creation and removal. We show that CR-UOT incorporates unbalanced Gromov-Wasserstein type problems through families of inner-product costs parameterized by linear transformations, enabling the matching of measures or point clouds across Euclidean spaces. We develop algorithms for such CR-UOT problems using entropic regularization and demonstrate that this approach improves the alignment of heterogeneous single-cell omics profiles, especially when many cells lack direct matches.