Yes you can do it in the root config.php file, but you’ll run into issues when you try to provision with tools like the great SequelPro Connector.

Instead create config.local.yaml in the root of your Chassis folder.

Then paste in this set of lines:

# Database configuration
# (When overriding, include all values)
database:
    name: wordpress
    user: wordpress
    password: vagrantpassword
    prefix: custom_prefix_

The last line is your custom database prefix and you should be off to the races.