>>"Can VDDUSB be set for 3.3V and VDDA be set for 1.8V for a PSOC6 device (CY8C62x7)?"
>>"Does the requirement VDDA must be the highest voltage present on the device still hold true for the VDDUSB rail?"
--> No. In case of PSoC 6 the power rails are independent. So there is no requirement for any voltage rail to be greater than or less than the other voltage rail. However there are few exceptions.
VDDIO should be greater than or equal to VDDA when using CapSense in the design. CapSense signals can switch between VSSA and VDDA, thus requiring VDDIO to support the swing to VDDA. In addition, the presence of VDDA without VDD or VDDD can cause some leakage from VDDA. However, it will not drive any analog or digital output. All the VDDA pins in packages that offer multiple VDDA supply pins must be shorted externally on the PCB.
Please refer PSoC 6 Hardware design considerations application note for more information.
>>"Do all PSOC6 devices require ports 9 and 10 to be tied to the VDDA rail?"
--> Please note that the power supply for the ports 9 and 10 is supplied by VDDA. This is the architectural design. So if you dont supply power to VDDA the ports 9 and 10 will not work along with the analog peripherals.
Hope the above information answers your questions.