A fundamental hindrance to building data-driven reduced-order models (ROMs) is the poor topological quality of a low-dimensional data projection. This includes behavior such as overlapping, twisting, or large curvatures or uneven data density that can generate nonuniqueness and steep gradients in quantities of interest (QoIs). Here, we employ an encoder-decoder neural network architecture for dimensionality reduction. We find that nonlinear decoding of projection-dependent QoIs, when embedded in a dimensionality reduction technique, promotes improved low-dimensional representations of complex multiscale and multiphysics datasets. When data projection (encoding) is affected by forcing accurate nonlinear reconstruction of the QoIs (decoding), we minimize nonuniqueness and gradients in representing QoIs on a projection. This in turn leads to enhanced predictive accuracy of a ROM. Our findings are relevant to a variety of disciplines that develop data-driven ROMs of dynamical systems such as reacting flows, plasma physics, atmospheric physics, or computational neuroscience.