Yes you will have to modify the variants.cpp file if you want to change the mapping of Serials and the SPI pins. First though I’d check for other variants / boards with the SAMD21G18 chip which maybe have the mapping you want in the variant folder.
The Adafruit guide tells you how to add / modify the SERCOM peripheral mappings for SPI and UART etc: Overview | Using ATSAMD21 SERCOM for more SPI, I2C and Serial ports | Adafruit Learning System
If you want a custom board you can also create a new variant folder in the framework and tell PlatformIO
board_build.variant = new_variant_folder
as seen in the above linked documentation.