All the hardware files that Cypress provide for FX3 Explorer Kit are present in the "SuperSpeed Explorer Kit Hardware Files" in the attached location, kindly refer.
All the HW files are in Cadence format. Why do you need Altium template for Motherboard? You can get the board dimension from Gerber file.
It would just make it easier. Some companies like Avnet provide a template that you can just place in Altium.