Fixes topLevel dependencies (#6712)

## What's the problem this PR addresses?

I noticed while refactoring code that one test wasn't correct, and was
hiding a bug in PnP. The locator `{name: null, reference: null}` was
returning different dependencies than `{name: "root", reference:
"workspace:."}`, which isn't expected.

## How did you fix it?

Refactored how we assign the `null` / `null` package entry - it's now
handled directly into `generateSerializedState` rather than the caller.

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