Motivation
In #184 I actually misunderstood the issue; basically we deliberately don't merge dictionaries because otherwise it would be annoying to the user if they've got their own config and we try and mess with it. This might relate to #58. So basically, our current approach is "if any config at all exists, leave it alone". And I think that's a reasonable policy but we should document it.

There is some thinking needed around this - it may be true to pyproject.toml config but there are some exceptions like ruff rules, dependenices etc.

Summary of desired enhancement
Document the fact that existing config is left untouched in general.