Right. There is some degree of transformation which is normal or necessary. For example, if one of {video, audio} is 24fps and the other is 23.976fps, the video will have its frame rate adjusted to match the audio. For basic video/audio mismatches you may need to trim audio, insert null audio, or add a mkv container delay.

These things are normally detailed in release notes. People write pretty detailed notes laying out exactly what they did.