Within the movie, is there a logical (non - "mystical" cop out) explaination for Neo's ability to see, feel and control machines in the real world?

In M2 the Architect says that if Neo chooses the 'left' door (which he does) everyone connected to the Matrix will perish.  They didn't (save only by Smith's hand) so what was he ranting on about then? Was it just idle threat used to create a wanted out come or did some weird unexplained thing happen to make this times choise of "the one" screw up...

How was Smith a direct threat to the Machine God?
He hated the Matrix but where else could he go after choosing exile? If he chose to destroy the Matrix then he himself would also perish. Yes he is bad, yes he is angry, but what exactly could he do apart from becoming the ruler of the  place here he can stant to be...?

In my first reading of Matrix III, the ending was so obvious and simple
that the Bad can never win the Good, Smith was finally defeated by the
machine easily. The logic is not that simple. The clue is
"purpose" and "choice". Neo lives with choice, he chooses to go back to
the machine city and fight for Zion. He is not programmed to do this,
even Oracle is not sure about his choices. Smith survives with purpose.
His purpose is to encounter and defeat Neo. However Smith's purpose was
programmed by Oracle/the Matrix. Smith thought that he had overcome it
because he has become an independent program - a virus. He has
controlled Oracle and after all he has infected all programs in Matrix.
Therefore, you  have seen all his copies in Matrix in the final fight
scene. The trick is the little girl if you remember the first scene
Mobil Ave. Do you remember what's the name of the little girl's parents?
What are their program functions? Her father is a recycle program while
her mother is an interactive program. Remember also that they have to
stay in the Mobil Ave - the nowhere place between reality and Matrix in
order to exchange for their little girl's survival? Also, the important
message is that no program can survive without a purpose according to
the recycle program - her father. Therefore they must save their
daughter by making a deal with the Frenchman so that the little girl
will not be deleted. This is the core meaning of Matrix III - all
program must be deleted if it doesn't have a purpose. A program remains
a program if it only lives with a purpose. This is the logic of Matrix
as well as its structure - the architect's work. Smith was borne with
Neo, they are the polarity of the balancing equations in Matrix. The
Architect (the white hair gentlemen, father of Matrix) constructed
Matrix through calculating balance equations while Oracle manages Matrix
by disordering it. This is the sixth experiment she made with Matrix.
You have to refer this to Matrix II. Neo was a part of Oracle's
construction, he is a program, a perfect program. But this is also a
fatal one. In order to balance  Matrix's environment, Smith was borne
because of balancing an equation that  disordered, which is Neo. Smith
must come with Neo, they are the other side of a same
body/program/existence. The stronger Neo becomes, the same with Smith.
Smith cannot be defeated without losing Neo. Oracle cannot control Neo
by deleting him to save Zion or the machine city because this is what
she believes - freedom and choice - the only way to maintain Matrix and
the human race. Neo did make a choice of his own. He knows that he must
save Zion and Matrix by scarifying himself. This is also the purpose of
his survival in Matrix. He cannot be deleted because he has a purpose to
stay in the system. Smith has a strong purpose to stay in Matrix as
well, he has to and be able to survive as long as there is an opponent
in the system. On one hand he can infect all programs in the system
because of his purposive existence, on the other hand he cannot be
deleted by the system itself because of that logic. Finally Smith can
have  power to even get control of the system. This is just like when
our computer is infected by a very strong virus and finally our system
hanged and can only be loaded with a infected/out-of-control program.
Oracle plays a very dangerous game which is "allow" Smith to get control
of her and soon the whole Matrix was infected by Smith. This is the only
way to end Smith. Once Smith has cleared everything of his way including
his own system, his purpose will be finished. "Everything has a
beginning and everything has an end." Smith will have no purpose to stay
once he has cleared up everything including Neo. The machine is able to
strike Smith through Neo's body with the tricky function of the little
girl's stay. There are only two programs which was never infected by
Smith or will not be wholly destroyed with the defeat of Smith which is
- the Recycle program and the Interactive program that left in the Mobil
Ave. They are enough to reboot the system and recycle what is remain to
make the system running in a "normal" way. This clue is so vague but it
is the most important point of Matrix III. Without understanding this
clue, the ending is simply any hollywood cliche.