This is stated again and again on HN, but it is just not true. You could run interpreted code, it just wasn't allowed to download and run modules, everything had to be linked into the application.
That said, there was talk about moving Wax to llvm-lua such that the resulting application would be compiled machine code. The new clause precludes this option entirely.
The only uncertainty left, now, centers around enforcement. There are a number of PhoneGap and Wax powered apps already in the store, and PhoneGap was even blessed as an approved framework. Only time will tell if that blessing stands.