What problem does this feature solve?

CLI options like skipping git -n, --bare or --registry are not configurable in the preset / file.
But ALL above options would make sense in a preset, as these are typically things configured on a project basis.

The command line option would always take precedence over the settings in preset file

What does the proposed API look like?

I.e. preset file could look like:

{
    "useConfigFiles": true,
    "git": false,
    "bare": true,
    "registry": "private-registry-url"