Sorry, I haven't had time to test anything. I think this might actually be the correct fix:
Put the packages in
assets/mycomponents/yourcomponent/_build/data/packages/ (you'll have to create the packages directory)
Change this line in the sources array in build.transport.php
'packages' => $root . 'core/packages',
to this:
'packages' => $root . '_build/data/packages',
Change this line:
$hasSubPackages = is_dir($sources['data'] . 'subpackages');
to this:
$hasSubPackages = is_dir($sources['data'] . 'packages');
After doing this, you no longer need the subpackages directory and you don't need to put the package files anywhere else.
Let me know if it works.