What can the Spy Bot do in Auto? Can it interfere with other robots? Can it score / damage the tower? Can it breach?
It can have a ball and score it. It can also “breach” the defense.
Seems pointless to cross a defense from the spy bot position.
Is having a ball implied or explicit?
And given sufficient prediction of the opponent’s actions (and given that most teams can’t autonomously sweve) can I place my robot such that it is an opponent robot’s autonomous path, halting their driving and preventing them from scoring? Can I place my robot somewhere else then program it to move into the opponent’s robot’s autonomous path?
From 3.4.2 I do not think you can place your robot in your own courtyard before the match.
Spy bots are placed in your opponents’ courtyards.
From 3.2
“A. pre-load one (1) BOULDER in or on their ROBOT such that the BOULDER is fully supported by their ROBOT…”
A spy can start with a ball, because this rule doesn’t state(nor does any other rule) that a spy can’t have a ball. Only special thing about spies is where they start the match.
Also, you can’t play a robot in your zone, so it is impossible to block an opponents path without breaking G13.
You could go out, get fully into the neutral zone, and then go back to the courtyard to get points for weakening one of the defenses. And while you’re in the neutral zone, pick up a ball for your 2-ball auto. 
Is it possible (rule wise not practically) that you can shoot and then go cross a defense? That’s shoot, and go back through a defense then return over or under it?
That seems like a much more practical way of doing the shot + Cross auto from a programming standpoint.
+1, if you are crossing back to get a ball from the mid-line.
Is there no specification of the spy bot in any other part of the rule book.
Please read the manual and tell us what you think. You can use the find function and the phrase spy bot if you already read it but don’t remember where the phrase was used.
Also, I’m not sure if that was a question, it sounded like one but it was ended with a period. Can you be more clear in your meaning?