Referring to the Intel Agilex® 7 FPGA I-Series Development Kit schematic diagram, link : /content/dam/support/us/en/programmable/support-resources/bulk-container/support/boards-kits/agilex/agilex-agi027-devkit-schematic-reva1-apr2021.pdf on page 2, you will see that there is a USB PHY device connected to the Intel MAX 10 device in the block diagram. However, the USB PHY device is not available on the development kit.
The USB PHY device has been replaced by Infineon (formerly Cypress) EZ-USB FX2 USB 2.0 Peripheral Controller. All USB PHY function and USB2.0 controller is implemented in the FX2 controller. The block diagram will be updated in a future release.