Non-working Adafruit SPIFlash configuration for Serpente R2

sketch.ino

/*
 * Print size, modify date/time, and name for all files in root.
 */
#include <SPI.h>
#include "SdFat.h"
#include "Adafruit_SPIFlash.h"


/*
#if defined(__SAMD51__) || defined(NRF52840_XXAA)
  Adafruit_FlashTransport_QSPI flashTransport(PIN_QSPI_SCK, PIN_QSPI_CS, PIN_QSPI_IO0, PIN_QSPI_IO1, PIN_QSPI_IO2, PIN_QSPI_IO3);
#else
  #if (SPI_INTERFACES_COUNT == 1 || defined(ADAFRUIT_CIRCUITPLAYGROUND_M0))
    //Adafruit_FlashTransport_SPI flashTransport(SS, &SPI);
    Adafruit_FlashTransport_SPI flashTransport(16, &SPI);
  #else
    //Adafruit_FlashTransport_SPI flashTransport(SS1, &SPI1);
  #endif
#endif*/

#define SPI_INTERFACES_COUNT 2 // was 1

#define PIN_SPI_MISO         (2ul) // PA06
#define PIN_SPI_MOSI         (0ul) // PA04
#define PIN_SPI_SCK          (1ul) // PA05
#define PERIPH_SPI           sercom0
#define PAD_SPI_TX           SPI_PAD_0_SCK_1
#define PAD_SPI_RX           SERCOM_RX_PAD_2

// SPI FLASH
#define PIN_SPI1_MISO        (12ul) //  PA18 // D12  //     PA18 FLASH_MISO // D12
#define PIN_SPI1_MOSI        (11ul) //  PA16 // D11  //     PA16 FLASH_MOSI // D11
#define PIN_SPI1_SCK         (9ul)  //  PA17 //  D9  //     PA17 FLASH_SCK  //  D9
#define PIN_SPI1_SS          (10ul) //  PA15 // D10  //     PA15 FLASH_CS   // D10

#define PERIPH_SPI1          sercom3 // serpente r2 schematic
#define PAD_SPI1_TX          SPI_PAD_0_SCK_1 // tnr checked datasheet e18a: sercom3 pad 0
#define PAD_SPI1_RX          SERCOM_RX_PAD_2 // tnr checked datasheet e18a: sercom3 pad 2


SPIClass mySPI = SPIClass(&PERIPH_SPI1, PIN_SPI1_MISO, PIN_SPI1_SCK, PIN_SPI1_MOSI, PAD_SPI1_TX, PAD_SPI1_RX);
Adafruit_FlashTransport_SPI flashTransport(PIN_SPI1_SS, &mySPI);
Adafruit_SPIFlash flash(&flashTransport);

// file system object from SdFat
FatFileSystem fatfs;

FatFile root;
FatFile file;

//------------------------------------------------------------------------------
void setup() {
  Serial.begin(115200);

  // Init external flash
  flash.begin();

  // Init file system on the flash
  fatfs.begin(&flash);
  
  // Wait for USB Serial 
  while (!Serial) {
    SysCall::yield();
  }
  
  if (!root.open("/")) {
    Serial.println("open root failed");
  }
  // Open next file in root.
  // Warning, openNext starts at the current directory position
  // so a rewind of the directory may be required.
  while (file.openNext(&root, O_RDONLY)) {
    file.printFileSize(&Serial);
    Serial.write(' ');
    file.printModifyDateTime(&Serial);
    Serial.write(' ');
    file.printName(&Serial);
    if (file.isDir()) {
      // Indicate a directory.
      Serial.write('/');
    }
    Serial.println();
    file.close();
  }
  
  if (root.getError()) {
    Serial.println("openNext failed");
  } else {
    Serial.println("Done!");
  }
}
//------------------------------------------------------------------------------
void loop() {}

From https://github.com/adafruit/Adafruit_SPIFlash/blob/master/examples/SdFat_ReadWrite/SdFat_ReadWrite.ino incorporating wa1tnr/conversations@28b51e6#diff-f1ad9a8852f791db9101cf6a23122b7d