My cinema employment, which briefly included Sony D-Cinema projectors, ended almost a decade ago so this is based on distant memories.
All preshow content (adverts, trailers, cinema idents etc.) was1:1.85 (flat) as they were when on film.
The D-Cinema playlists were setup with the commands to tell the projector to switch to the desired aspect ratio. So you would have a 1.85 command at the start of the playlist for the adverts, trailers etc. and then another command to switch to the aspect ratio of the feature.