The example project BootLedBlink makes use of APIs in the boot library whereas the example project UsbSpiDmaMode makes use of APIs in the firmware library. It is not recommended to use boot library and firmware library together in a project.
I understood that your intention is to use a GPIO in the project UsbSpiDmaMode . For this, you can refer to the SDK example cyfxgpioapp. This project makes use of firmware library and can be found in the following location of FX3 SDK:
C:\Program Files (x86)\Cypress\EZ-USB FX3 SDK\1.3\firmware\serialif_examples
Please merge this project with UsbSpiDmaMode to develop your end application.