TLDR; use the POOL and COM ports via spade connectors
The IntelliConnect has two two-pair RS485 connectors (For the IntelliFlo VS pump and IntelliChlor salt cell), and then it has a two-pair connector for "temp," and a two-pair connector for "Heater".
That said, and to your point, only the RS485 connectors connect via the Green/Yellow data cables to the respective hardware. The temp probe connects directly, and the Pentair UltraTemp Heat Pump connects to the POOL and COM ports via spade connectors.