What he's saying is that if you had (say) a FS image with nginx, mysql, and rails installed on it, the system has no idea of what files belong to mysql and what files belong to rails. So you wouldn't just be able to take said image and tell OSTree "remove mysql and replace it postgresql".

Docker works in a really similar way, actually -- it creates file system images and tars them up, and then uses AUFS to separate changes in each container from the base image. Docker added metadata to describe how to build images; if you want to change the components (AFAICT) the "right" way is to change the metadata and then do a full rebuild.