You'd have to modify the build.transport.zip file to do it. You can specify any source and target directories and you can have as many file resolvers in build.transport.php as you like. Modify the $sources array near the top of the file to add the new source directories and do something like this:
if ($hasAssets && $i == 1) {
$helper->sendLog(MODX::LOG_LEVEL_INFO, 'Packaged some assets directory files');
$vehicle->resolve('file',array(
'source' => $sources['extra_source_assets'],
'target' => "return MODX_ASSETS_PATH . 'somedirectory/';",
));
$helper->sendLog(MODX::LOG_LEVEL_INFO, 'Packaged some more assets directory files');
$vehicle->resolve('file',array(
'source' => $sources['other_source_assets'],
'target' => "return MODX_ASSETS_PATH . 'some_other_directory/';",
));
// of if you want the files directly under the MODX assets directory:
$helper->sendLog(MODX::LOG_LEVEL_INFO, 'Packaged assets directory files');
$vehicle->resolve('file',array(
'source' => $sources['some_other_source_assets'],
'target' => "return MODX_ASSETS_PATH;",
));
}
Note that in the older verion of MyComponent, you can also transfer packages (e.g., TinyMCE) as packages, which you can then search locally for in Package Manager and install, though you give up notifications of updates since they didn't come from the MODX repo. TBH, I can't remember if this option works in the current version. It did at one time, but I haven't tested it since I refactored MyComponent and can't remember if I finished it.
Being able to name packages in the config file and have them automatically installed with no further work is on the Roadmap, but probably won't come any time soon.
You don't want to mess with the locations of the core files or the Lexicon won't work. If you were creating a package for submission as an extra, I'd strongly recommend against moving assets files, but I can see why you might want to do it for your own use. I like having them in the standard locations (under assets/components/component_name) because it makes it easier for me to write code that will work in both the development and installed versions, makes it easier for folks to find them, and keeps the assets directory less cluttered.