[migration] `pyrefly init` has at least some gaps

[stroxler]

Describe the Bug

I only know of one gap right now, but we can add to this issue if we find more.

When migrating a mypy project that had ignore_missing_imports set, we didn't get replace_imports_with_any and we should have

Sandbox Link

No response

(Only applicable for extension issues) IDE Information

No response

[yangdanny97]

we don't insert a newline before the additions to pyproject.toml, so for the config files that don't end with newline it won't work