I would wager that it has to do with the way that it gets compiled, if they aren't using Apple's compiler and profiler they may not be taking advantage of the APIs needed to do all that super neato app backgrounding and such.
You call the timing dubious, I say they are pre-emptively stopping thousands of app rejections on a legit rule.
You are bashing Apple for making a system you aren't forced to buy and complaining that you can't 'hack' it in your language of choice. Apple doesn't care about JailBreaking anymore than the bare minimum for legal reasons, if you want to run any old app you can, no Apple approval required.
Fact of the matter is, Apple is a company that makes more money in an hour than you do in 10 years, they aren't stupid people.