Conceptually, I don't see how this is much different from JIT compilers in the JVM, CLR, and similar runtimes. You don't hear so much from Java devs about how they can't* see the machine code their customers are running. They talk about cold-start performance, but accept that the first few requests will be slower in exchange for the productivity and eventually-high-performance.
Now that I think about it, this is how V8 works too, for JS code itself!
Why wouldn't this principle apply to bundling?