I gave Menno this answer (and modified the Mycompopnent docs), but for others who find this:
First, the subpackages go in assets/mycomponents/yourcomponent/_build/subpackages, not assets/components ...
Second, for safety, MyComponent won't overwrite an existing project's build.transport.php file because the user might have made important mods there. If a new version makes changes to that file (like 3.1's new subpackage code) you need to update it manually. If you haven't made any mods to it, you can simply delete it and run Bootstrap (or copy the file from the core/components/mycomponent/elements/chunks/ directory).
If you have modified it, you'll have to either merge the new code into your existing file, or vice versa.
Any new projects will get the new build.transport.php file automatically, so this only applies to existing ones (in this case, only to existing projects with subpackages).
Sorry for any confusion.