I think the current best practice is to not run Composer on the target production server. The regular process of deploying a web application usually requires several independent steps, and Composer is only suitable for some of them, regardless of what people make it do additionally.
You mention minification, and I would add the process of pulling in JavaScript dependencies in general. This is no domain for Composer. It has been done in the past to offer Composer packages that contain Jquery, but this requires additional work to put Jquery in the right directory afterwards, adding the need to run post install scripts or add installers that need configuration. I guess the right way to do it would be to use Bower for this.
So the deployment would be at least a three step process.
- Use composer to install PHP dependencies.
- use bower to install JavaScript dependencies.
- Use rsync, SFTP, SCP or FTP(S) to move all the files to the server.
Any optimization steps would be done prior to moving the files onto the server inside the deployment script.
And if anything fails during the collection of dependencies, be it an unsuspected downtime of Github, or your deployment server running out of disk space, you don't end up with a halfway deployed new website version. You can stop the deployment script before syncing if anything is missing or gone wrong.