Stable glasses (SGs) are formed through surface-mediated equilibration (SME) during physical vapor deposition (PVD). Unlike intermolecular interactions, the role of intramolecular degrees of freedom in this process remain unexplored. Here, using experiments and coarse-grained molecular dynamics simulations, we demonstrate that varying dihedral rotation barriers of even a single bond, in otherwise isomeric molecules, can strongly influence the structure and stability of PVD glasses. These effects arise from variations in the degree of surface mobility, mobility gradients, and mobility anisotropy, at a given deposition temperature (Tdep) At high Tdep, flexible molecules have access to more configurations, which enhances the rate of SME, forming isotropic SGs. At low Tdep, stability is achieved by out of equilibrium aging of the surface layer. Here, the poor packing of rigid molecules enhances the rate of surface-mediated aging (SMA), producing stable glasses with layered structures in a broad range of Tdep. In contrast, the dynamics of flexible molecules couple more efficiently to the glass layers underneath, resulting in reduced mobility and weaker mobility gradients, producing unstable glasses. Independent of stability, the flattened shape of flexible molecules can also promote in-plane orientation orderat low Tdep. These results indicate that small changes in intramolecular relaxation barriers can be used as an approach to independently tune the structure and mobility profiles of the surface layer and thus the stability and structure of PVD glasses.