I tried to build atsam gateway without USB support and had the problem that the sercom pointer were not initialized. The problem is that without the "USBCON" define, “__libc_init_array()” is not called within the MyMainSAMD.cpp main(). After moving “__libc_init_array()” out of the “USBCON” condition, everything works fine.

/*
 * The MySensors Arduino library handles the wireless radio link and protocol
 * between your home built sensors/actuators and HA controller of choice.
 * The sensors forms a self healing radio network with optional repeaters. Each
 * repeater and gateway builds a routing tables in EEPROM which keeps track of the
 * network topology allowing messages to be routed to nodes.
 *
 * Created by Henrik Ekblad <henrik.ekblad@mysensors.org>
 * Copyright (C) 2013-2020 Sensnology AB
 * Full contributor list: https://github.com/mysensors/MySensors/graphs/contributors
 *
 * Documentation: http://www.mysensors.org
 * Support Forum: http://forum.mysensors.org
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * version 2 as published by the Free Software Foundation.
 */

// Initialize library and handle sketch functions like we want to

extern "C" void __libc_init_array(void);

int main(void)
{
	init();   
        __libc_init_array();      // after
#if defined(USBCON)	
//        __libc_init_array();     before
	USBDevice.init();
	USBDevice.attach();
#endif
	_begin(); // Startup MySensors library
	for(;;) {
		_process();  // Process incoming data
		if (loop) {
			loop(); // Call sketch loop
		}
		if (serialEventRun) {
			serialEventRun();
		}
	}
	return 0;
}

I don't know why it is within the condition and if it is good to move it outside, but it seems to work.