Yes, but you can still write to the port registers directly. Using the Arduino libraries doesn't lock you out of anything. There's a smooth, continuous path from high-level C++ abstractions built on the Arduino primitives down to the bit-twiddling low-level C world.

If you're walled off in a Javascript VM, you can never have that kind of transparent access to the hardware - which seems like a big problem when you are building electronics, and controlling the hardware is the entire point of the job.