Third-party packages are usually interfaced, and developing interfaces is never as easy as the vendors claim. Second, even though the vendors provide interface utilities, no matter how well designed and tested they are, you will still encounter interface limitations and other issues.
As for interfacing ERP with shop floor systems versus PLM, you can generally expect a looser handshake between shop floor execution and the planning systems of ERP. This means the number, frequency and complexity of interfaces with MES software are likely less stringent than PLM. But this is not universally the case. It depends on the ERP software in question and the specific functions used in the third-party software.