You would have to create a new board type with its own "variant.cpp" that maps all of the pins you want to use. This will be comparatively easy, if you don't care about alternate functionality (ADC, Sercom, timers/pwm, interrupt, etc)
variant.cpp (and variant.h) are relatively obvious. For SAMD, there's a big array:
const PinDescription g_APinDescription[]=
{
// 0..13 - Digital pins
// ----------------------
// 0/1 - SERCOM/UART (Serial1)
{ PORTA, 11, PIO_SERCOM, (PIN_ATTR_DIGITAL), No_ADC_Channel, NOT_ON_PWM, NOT_ON_TIMER, EXTERNAL_INT_11 }, // RX: SERCOM0/PAD[3]
{ PORTA, 10, PIO_SERCOM, (PIN_ATTR_DIGITAL), No_ADC_Channel, NOT_ON_PWM, NOT_ON_TIMER, EXTERNAL_INT_10 }, // TX: SERCOM0/PAD[2]
// 2..12
// Digital Low
{ PORTA, 14, PIO_DIGITAL, (PIN_ATTR_DIGITAL), No_ADC_Channel, NOT_ON_PWM, NOT_ON_TIMER, EXTERNAL_INT_14 },
{ PORTA, 9, PIO_TIMER, (PIN_ATTR_DIGITAL|PIN_ATTR_PWM|PIN_ATTR_TIMER), No_ADC_Channel, PWM0_CH1, TCC0_CH1, EXTERNAL_INT_9 }, // TCC0/WO[1]
{ PORTA, 8, PIO_TIMER, (PIN_ATTR_DIGITAL|PIN_ATTR_PWM|PIN_ATTR_TIMER), No_ADC_Channel, PWM0_CH0, TCC0_CH0, EXTERNAL_INT_NMI }, // TCC0/WO[0]
:
:
// 38..41 - EDBG/Digital
{ PORTA, 13, PIO_PWM, (PIN_ATTR_DIGITAL|PIN_ATTR_PWM), No_ADC_Channel, PWM0_CH5, NOT_ON_TIMER, EXTERNAL_INT_13 }, // EIC/EXTINT[13] *TCC2/WO[1] TCC0/WO[7]
{ PORTA, 21, PIO_PWM_ALT, (PIN_ATTR_DIGITAL|PIN_ATTR_PWM), No_ADC_Channel, PWM0_CH7, NOT_ON_TIMER, EXTERNAL_INT_NONE }, // Pin 7
{ PORTA, 6, PIO_PWM, (PIN_ATTR_DIGITAL|PIN_ATTR_PWM), No_ADC_Channel, PWM1_CH0, NOT_ON_TIMER, EXTERNAL_INT_NONE }, // Pin 8
{ PORTA, 7, PIO_PWM, (PIN_ATTR_DIGITAL|PIN_ATTR_PWM), No_ADC_Channel, PWM1_CH1, NOT_ON_TIMER, EXTERNAL_INT_NONE }, // Pin 9
// 42 (AREF)
{ PORTA, 3, PIO_ANALOG, PIN_ATTR_ANALOG, No_ADC_Channel, NOT_ON_PWM, NOT_ON_TIMER, EXTERNAL_INT_NONE }, // DAC/VREFP
// ----------------------
// 43 - Alternate use of A0 (DAC output)
{ PORTA, 2, PIO_ANALOG, PIN_ATTR_ANALOG, DAC_Channel0, NOT_ON_PWM, NOT_ON_TIMER, EXTERNAL_INT_2 }, // DAC/VOUT
} ;
that maps "Arduino pin number" to everything else. Adding strictly digital pins would mean adding a bunch of lines similar to the line for pin2, probably at the end (so as not to conflict with existing boards.)