Fix it so disableKinds etc. does not get merged in from theme

Fix it so disableKinds etc. does not get merged in from theme

Unless the merge strategy is set up to do so.

For `disableKinds` the current workaround is to make sure the project config has an entry, even if is empty:

```
disableKinds = []
```

Note that this issue only touches root, non-map config-values that either is not set in project config or in Hugo's defaults.

Fixes #8866