[Native] Fix fallback atoms when writing to Native file.

There is no test as currently there is no call to the NativeWriter.

Future commits will add calls to the NativeWriter.
Fill the atom gap with INT 3 instead of NOP.

INT 3 (machine code 0xCC) will raise an interrupt when executed. That is better
for filling the gap than NOP because we want to stop the execution immediately
when the control reached to non-code address.