@Mario:

I don't have an Arduino Mega to test your program on bare metal.

However, I suspect that .hex generated by LDmicro based in yourtemp.hex.ld program is faulty:

1. You have NOT assigned any pin for PWM out; LDmicro variable list complains, under in name column: PAtemp PWM Out <not an I/O!>

2. You can NOT assign 60 Hz as base frequency for PWM in Arduino.
Available PWM target (base) frequencies in ATmega 164/324/644/1284/2560 follow this formula:
fPWM = fclk_I/O / (n*256) where fcIk_I/O is the frequency of external or internal oscillator, and n can be 1, 8, 64, 128 or 256, see https://github.com/LDmicro/LDmicro/wiki/LDmicro-PWM and

Arduino Mega has a 16 MHz crystal, so available PWM target frequencies are 62500 , 7812, 976, 488 and 244 Hz, far away from 60 Hz.

I suggest you: assign a suitable pin for PAtemp PWM Out (double click on PAtemp variable, and select an available pin), change the target frequency to a allowed value, then compile again and test...