SPI Mode 3 on Due doesn't work properly with new APIs i.e. using SPI.beginTransaction(SPISettings)

When I try to set SPI in Mode 3 on Due the first write doesn't work all the time. Upon investigating more I observed that when Due is set in Mode 3 the clock polarity on the oscilloscope is wrong for the cases it doesn't work on the first write, it generates Mode 0 clock.

The issue can be reproduced by using the following sketch to write to an EEPROM, the write in the setup function doesn't write correct data when the Clock of Mode 0 is generated when the SPI_Mode is set to Mode 3. However, the data written in the loop is read correctly and printed on Serial monitor when the:

```
#include
// Using simple SPI APIs for Due
#define CSPin 4
#define CLKRate 16000000
void setup() {
pinMode(CSPin ,OUTPUT);
SPI.begin();
digitalWrite(CSPin,HIGH);
Serial.begin(9600);
Serial.println("SETUP");
SPI.beginTransaction(SPISettings(CLKRate, MSBFIRST, SPI_MODE3));
digitalWrite(CSPin,LOW);

SPI.transfer(6);
digitalWrite(CSPin,HIGH);
SPI.endTransaction();
delay(10000);

Serial.println("SETUP:WriteData");
SPI.beginTransaction(SPISettings(CLKRate, MSBFIRST, SPI_MODE3));
byte dataWrite[8] = {2, 0, 0, 1, 3, 8, 4, 6};
digitalWrite(CSPin,LOW);

for(int i = 0 ; i < 7;i++)
{
SPI.transfer(dataWrite[i]);
}
SPI.transfer(dataWrite[7]);
digitalWrite(CSPin,HIGH);
SPI.endTransaction();
delay(10000);

Serial.println("SETUP:ReadData");
SPI.beginTransaction(SPISettings(CLKRate, MSBFIRST, SPI_MODE3));
byte dataWrite1[8] = {3, 0, 0, 0, 0, 0, 0, 0};
byte readData[8];
digitalWrite(CSPin,LOW);

for(int j = 0 ; j < 7;j++)
{
readData[j] = SPI.transfer(dataWrite1[j]);
Serial.println(readData[j]);
}
readData[7] = SPI.transfer(dataWrite1[7]);
Serial.println(readData[7]);
digitalWrite(CSPin,HIGH);
SPI.endTransaction();
Serial.println("ExitingSetup");
}

void loop() {
// put your main code here, to run repeatedly:
// Set BitRate to 4 MHz
Serial.println("LOOP");
SPI.beginTransaction(SPISettings(CLKRate, MSBFIRST, SPI_MODE3));
digitalWrite(CSPin,LOW);

SPI.transfer(6);
digitalWrite(CSPin,HIGH);
SPI.endTransaction();
delay(1000);
SPI.beginTransaction(SPISettings(CLKRate, MSBFIRST, SPI_MODE3));
byte dataWrite[8] = {2, 0, 0, 1, 3, 6, 4, 5};
digitalWrite(CSPin,LOW);

for(int i = 0 ; i < 7;i++)
{
SPI.transfer(dataWrite[i]);
}
SPI.transfer(dataWrite[7]);
digitalWrite(CSPin,HIGH);
SPI.endTransaction();
delay(1000);
SPI.beginTransaction(SPISettings(CLKRate, MSBFIRST, SPI_MODE3));
byte dataWrite1[8] = {3, 0, 0, 0, 0, 0, 0, 0};
byte readData[8];
digitalWrite(CSPin,LOW);

for(int j = 0 ; j < 7;j++)
{
readData[j] = SPI.transfer(dataWrite1[j]);
Serial.println(readData[j]);
}
readData[7] = SPI.transfer(dataWrite1[7]);
Serial.println(readData[7]);
digitalWrite(CSPin,HIGH);
SPI.endTransaction();
delay(10000);
}
```

Start at the SPI.beginTransaction(SPISettings) path and reproduce the provided sketch on an Arduino Due while observing the clock signal. The work is done when SPI_MODE3 consistently produces Mode 3 clock polarity on the first write, including the setup transaction, and the EEPROM receives the correct data.

Written by the indexing model from the issue text.