Twisting bilayers of transition metal dichalcogenides gives rise to a moiré potential resulting in flat bands with localized wave functions and enhanced correlation effects. In this work, scanning tunneling microscopy is used to image a WS2 bilayer twisted approximately 3° off the antiparallel alignment. Scanning tunneling spectroscopy reveals localized states in the vicinity of the valence band onset, which is observed to occur first in regions with S-on-S Bernal stacking. In contrast, density functional theory calculations on twisted bilayers that have been relaxed in vacuum predict the highest-lying flat valence band to be localized in regions of AA' stacking. However, agreement with experiment is recovered when the calculations are performed on bilayers in which the atomic displacements from the unrelaxed positions have been reduced, reflecting the influence of the substrate and finite temperature. This demonstrates the delicate interplay of atomic relaxations and the electronic structure of twisted bilayer materials.