Is there a way to prevent Lenovo System Update from installing some Packages (like the Toolbox) when the system is running in silent mode?

I plan to only install certain packages, for instance, Toolbox or Desktop Experience, and do not wish to have the rest done.

There are several ways that you can perform a customization for this...

Method 1:

Create your own repository with ThinkVantage Update Retriever, and then delete the updates you don't want from your own repository.

Method 2:

Create a web-based repository. According to the ReadMe here Thin Installer supports web-based repositories. Please refer to the deployment guide here before trying this.