The FleePath should definitely use penalties. Local avoidance however is pretty separate from pathfinding. Local avoidance cares, as the name implies, only about very local information. Penalties require something a bit more long term to actually make use of it. That's why you usually combine pathfinding and local avoidance to get the best of both.
Yeah. That is something that is on my TODO list though. I agree that it is not optimal that it ignores penalties.