After a long struggle with this problem, and observing no conclusive solution in many posts on both Ableton and Cycling74 forums, this is probably the beginning of another debate, but here at least is a solution that apparently works.
...If you are reading this, you probably already know the problem, but to summarize: many standalone and M4l applications use either externally developed binaries, or need access to files not in the patcher. These latter files may include poly~ subpatchers, coll data, pattrstorage data, audio media, video media, and other forms of 'local' data which is not stored inside the Max patcher itself. From one perspective, whether the file is another subpatcher, or a binary, or text data, or audio data, or a movie, should essentially make no difference in theory, as they are all 'external' files per se. In practice, as a build project needs to manage many other files besides the user's, the build process sorts external files for standalones, collectives, and M4L .amxd files, and handles each type slightly differenty.