The use of charts and manifests explained:
Kustomization with all its benefits as described in earlier posts also serves as a template free configuration
When the charts are authored they have to be general purpose with the user having the ability to specify the parameters for deployment. Most of these options are saved in the values file. Even if there are more than one chart, the user can provide these values to all the charts via a wrapper values file. These values are then used to override the default values that may come with the associated chart. The template allows taking these options from the values files and using it to create the Kubernetes resources as necessary. This makes the template work the same regardless of the deployment. The syntax used in the templates is quite flexible to read the options from the values file. Other than these parameters, the templates are mere static definitions for Kubernetes resources and encourage consistency throughout the definitions such as with annotations and labels.
When the charts are used with values file, kustomization is not necessary. It is just a value add on based on our discussion above. The user can choose between specifying manifests and charts to suit his deployment. They serve different purposes and it would behoove the user to use either or both appropriately.
The user also has the ability to compose multiple values files and use them together with comma separations when specifying to apply the chart. This allows the user to organize the options in the values file to be granular and then include them on a case by case basis.