Khan had no way of knowing the Enterprise was on the edge of Klingon space with the 72 missiles aimed at him, so he'd never have a chance to trigger a fail-safe. He couldn't even know there'd be a Scotty around to track the destination of the top-secret-prototype hand-held transporter. He'd have to have built proximity sensors and beacons into the missiles so they'd never explode and alert him when they've been launched - because Marcus could have launched them at anything. "See if you can take out that womp rat over there!" Boom - So much for Zed!
If Marcus' primary goal is war with the Klingons instigated by firing long-range sub-space missiles at the Klingon Home World, then he isn't going to test one against a target on the other side of the San Francisco Bay. You're also assuming that missiles that DIDN'T have Khan's crew inside weren't already used as part of a weapon demonstration Khan gave to Marcus at some point in the development process.
So relying on Marcus aiming these particular missiles at Khan would be a crucial strategic flaw. And in the movie Khan seemed SHOCKED that there were 72 missiles on the Enterprise - at which point he immediately surrendered. That action alone suggests it wasn't his plan all along to be targeted by the missiles. What if they only loaded 12? Then Khan kills Kirk and plan ruined?
Not if they're the only missiles in the Starfleet Arsenal that can be fired from a ship at a significant distance from Kronos. So I don't think it was the number, just that Kirk could fire them from a great distance away.
In the movie Khan also seems to be someone who Kirk can trust, complete with saving him during the space jump from the Enterprise to Marcus' ship. So just because Khan acts surprised doesn't mean he actually was. Knowing that he was Khan, I assumed in EVERY one of his interactions he was being deceptive.
I'm not sure we can assume that Khan always intended on ending up on Kronos either. What happens if he killed everyone at Starfleet HQ and Kirk doesn't trash his ship? Does he still transport out or does he try to find the torpedoes that contain his crew?
I think we can, again, ultimately, Khan seemed to be baiting Admiral Marcus completely. Marcus theoretically, could have said "well, he's on Kronos, let him rot there". And guess what, movie ends. This is one of those things where you have to draw the conclusion that if Khan's on Kronos and Marcus wants war with the Klingons because it's "inevitable" then, that's the reason why Khan went there.
Also, stealing a single portable transporter is a lot easier than stealing 72 missiles.
I don't want to start a huge fight, so at the end of the day I think we'll just have to agree to disagree. As the viewer of any movie, you can either fill in the blanks with connections that you come up with on your own or you can consider the movie flawed for not properly connecting all the dots or for making plot points too convenient. I guess it just comes down to how forgiving you are personally willing to be for the sake of enjoying something.