Currently, it isn't possible to add delay to TrueHD with eac3to (at least with Atmos), it's added to the filename instead, would it be possible to add that functionality (without breaking Atmos)?
My uneducated guess is that starting cutting/copying the second frame, rather than the first, might work, assuming the first one keeps the metadata. From my testing with Dolby Reference Player, trimming results in an error saying the desired presentation was not found, and duplicating with the first frame results in a stutter.