Its very common for themes sold on themeforest to include packaged premium plugins, and in fact it is required if that plugin is sold on themeforest too. As far as WooCommerce, that should not of been included unless they modified it in some way.
The only way I can think of to interact with Envato and download a purchase is via the API but I am not aware of anything that makes this work with Composer specifically, and even if it did, you would only be able to manage the theme itself since buying the theme doesn’t give you access to the actual plugins on the market.
As far as install, they are supposed to be using TGM Activation for all plugin integration if it is sold via Themeforest, So that is probably what it is using, and it sounds like there is a permissions error when it attempts to access the folder they are stored in. TGM uses the standard WP plugin system to install stuff, so I doubt there is a problem there. Either way it doesn’t care where you put them, as long as they are installed.
In short, there is no easy way since you don’t have direct access to all the plugins, only the versions packaged with the theme. It may be best to solve your permission issue, but if you want to use composer you will probably have to maintain a private repo of the entire theme and update it as updates are made available by the author. There is quite an extensive discussion about this here.
HTH