What about 3rd party licenses required for the commercial use of traits or certain biological materials? Does the ILP provide for full freedom-to-operate?

The ILP only provides a license to patents owned or controlled by its Members. If additional licenses (e.g., for certain enabling technologies or 3rd party traits) are necessary for the use of a trait or biological material it is the duty of the Licensee Member to obtain such licenses. Of course a Licensee Member can ask the Patentee Member whether patents from third parties apply.