fix: Fix that pyproject.toml is continuously outdated in certain cases

[NiklasRosenstein]

Sometimes the pyproject.toml would add or remove some newlines, in certain cases also be continuously outdated, never satisfying the pyproject.check task. This is because we converted the top-level tomlkit container that keeps track of formatting to a standard Python dict.

[NiklasRosenstein]

Now that we're using a MutableMapping as the base class for Pyproject since #223, setdefault() behaves differently as explained in python-poetry/tomlkit#49 (comment).

Need to override setdefault(), although I fear we might hit other incompatibilities issues down the road.. (This is the second, after #223).