The following four questions assume that there is a valid route connecting Milano and Venezia, that the Ferdinandea Succession does not occur, and that the game is in phase four.
(a) 3.3.4, bullet 2: Is it legal in phase four to start a corporation with a token inside the yellow border of Austria? [Rule 3.3.4 seems to indicate that it is not legal.]
As said by beckerc, you can start a company anywhere on the map (except Swiss territory) in phase four, so this is fine. Note, however, that you can't start a major partially inside and partially outside Austria, as then its two bases would be separated by an active border (3.3.4).
(b) 3.3.4: Is it legal for the IRSFF to start corporation B with all or corporations B's tokens outside the yellow border of Austria?
YES. Unequivocally. You can even buy its tokens assuming you can trace a route there from an IRSFF token outside of Austria.
(c) 4.2: Assume that the IRSFF has a valid route from Milano to Parma without crossing the yellow Austrian border. May the IRSFF lay a token in Parma? [The token laying rule 4.2 seems to indicate that this would be legal.]
Correct. You have to be able to trace a route from one of your tokens to where you want to place one without crossing an active border, so you're good.
(d) 4.2: Assume that the IRSFF has a valid route from Milano to Parma which does cross the yellow Austrian border. May the IRSFF lay a token in Parma? [The token laying rule 4.2 seems to indicate that this would not be legal. However, the IRSFF is actually operating in both countries.]
No never ever. You must have some route from one of your tokens to where you want to lay a token that does not cross an active border: not even if it does it twice.
Note that I'm disagreeing with beckerc on b,c, and d. I think he misinterpreted b, but I'm actively disagreeing with c and d.