When deploying the software the person deploying the platform creates the site-config directory to store files that have been modified to control the installation and configuration of the software. The sas-bases directory is where the files that SAS provide are stored.
There are a few examples in the SAS documentation of how to organize the site-config directory but it is ultimately up to the person deploying the software to order it in a way that makes sense for your organization. Please see the link below for further information about the SAS suggested directory structures:
SAS® Viya® Platform Operations - Deployment - Directory Structure
I can't see a reference to a 'vdm' directory in the SAS documentation but it could perhaps be related to 'SAS Visual Data Mining'. If you can provide some further information about the YAML files it contains it will be easier to identify what it is being used for.
Many thanks,
Jack