Creating variable inside if statement (conditional signed vs unsigned int)
You could try something like this:

int16_t readRegister(byte thisRegister) {
  int16_t result;

  // take the chip select low to select the device:
  SPI.beginTransaction(SPISettings(2500000, MSBFIRST, SPI_MODE3));
  digitalWrite(SlaveSelectPin, LOW);

  //now get the value
  result = SPI.transfer16(thisRegister);

  // finish up
  digitalWrite(SlaveSelectPin, HIGH);
  SPI.endTransaction();

  // return the result:
  return (result);
}

uint16_t readUnsignedRegister(byte theRegister) {
  return (uint16_t) readRegister(theRegister);
}


Another alternative is to define a "universal" data type, i.e. a union and necessary cast operators.

union univ16_t {
  uint16_t as_uint16;
  int16_t as_int16;

  univ16_t(int value)
  {
    as_int16 = value;
  }

  operator uint16_t()
  {
    return (as_uint16);
  }

  operator int16_t()
  {
    return (as_int16);
  }
};


This allows the function to have the following form:

univ16_t readRegister(byte thisRegister) {
  int result;

  // take the chip select low to select the device:
  SPI.beginTransaction(SPISettings(2500000, MSBFIRST, SPI_MODE3));
  digitalWrite(SlaveSelectPin, LOW);

  //now get the value
  result = SPI.transfer16(thisRegister);

  // finish up
  digitalWrite(SlaveSelectPin, HIGH);
  SPI.endTransaction();

  // return the result:
  return (result);
}


With the two possible assignments. 

uint16_t reg1 = readRegister(...);
int16_t reg2 = readRegister(...);


Cheers!