I think the answer is definitely yes. Apple's software engineering is not that great. There is always some hole in Safari that allows root access to the entire device. They can't get atomic syscalls working in OS X. Does anyone really think they can recruit and afford people that can tell computer-generated software from hand-written software?
My guess is that this is a scare tactic to keep anyone thinking of supporting two platforms at once to "not want to risk it" and go for the iPhone instead. More users, only so many hours that the developer can be awake, safer to just go with the iPhone. (Of course, you are already risking it anyway; use the wrong multi-touch gesture -- app denied. Use a Google service -- denied. Do something useful that Apple wishes they thought of first -- denied. And people wonder why there are so many fart apps...)
My next guess is that this tactic will be successful. People seem to adore doing whatever Apple tells them to do. It frightens me.
What I've learned from iPhone vs. Android (among other things) is that people will pick pretty and mean over average and nice.
I'd expect many languages and frameworks are going to have many very signature functions and patterns of code. If Apple decides to enforce this, they won't have a hard time.
On top of that, if they miss it, and let a bunch of apps in, then later on determine those apps were crosscompiled, they can revoke the current versions and block that developer...
Have you filed a bug?
Is this the kind of company you want to build software for? This is bullshit. Do I really even want to play along anymore?
This company makes great products, but they can do completely dickish things.
I wonder if the open source world can successfully fight back, by making compilers that generate code the app store police can't tell from hand written.