The Transporter vs Agent 47

47 is hired to kill a mob boss who is being transported from Johns Hopkins in Baltimore to the US Capitol in Washington DC. Martin is hired to get the mob boss to the Capitol safely using whatever means necessary, and knows an expert assassin is coming after him, although he doesn't know the specifics. 47 also knows the mob boss is being transported by an expert driver, but doesn't know the specifics.

Does 47 kill his target, or does Frank protect him?

I'll side with 47. Much easier for him to kill someone Frank's guarding than to kill Frank himself.

What if he was coming after Frank himself? What if he was hired to kill Frank, and Frank meanwhile hears through the grapevine that an expert assassin is coming to kill him. How would this go?

Still would give the advantage to 47. Assassination is his profession.

True. The only reason he didn't die in the first film is because a vending machine coincidentally malfunctioned.