The present disclosure relates to systems, methods, and non-transitory computer readable media for accurately and flexibly generating modified digital images utilizing a novel swapping autoencoder that incorporates scene layout. In particular, the disclosed systems can receive a scene layout map that indicates or defines locations for displaying specific digital content within a digital image. In addition, the disclosed systems can utilize the scene layout map to guide combining portions of digital image latent code to generate a modified digital image with a particular textural appearance and a particular geometric structure defined by the scene layout map. Additionally, the disclosed systems can utilize a scene layout map that defines a portion of a digital image to modify by, for instance, adding new digital content to the digital image, and can generate a modified digital image depicting the new digital content.