Probably I'm too late to reply to this topic, but I'm also looking forward to seeing SFTP for each application.
I need SFTP access mainly for WordPress and ghost for theme tweaks and updates.
For the moment, I use Transmit app and login with VPS root just for updating theme files.
So it would be great if I can use app-specific SFTP for security.
(There's already unmanaged Wordpress, but I like the managed WordPress app which separates Wordpress core from theme and plugins. )