Thanks for the update, now the behaviour is consistent between hw=give_way/stop, hw=traffic_signals and traffic_sign=* in the middle of a single way. That’s good!
But it’s still not perfect IMHO 
In this image, there are hw=give_way hw=stop, hw=traffic_signals and traffic_sign=* nodes in row 1 and 3. In row 2 the same are part of a continuous way going left to right (W->E). The white arrows are from a drawing style “Ausrichtung / Direction” by Hanikatu.
For all of the nodes, I moved the mouse to the left and pressed “H”.
The first row gave me what I think are perfect results: The direction arrow points left, indicating from which direction the sign / light can be seen and also for which direction it is relevant.
The second row resulted in all the nodes getting a “backward” direction, meaning the signs and light are now relevant for traffic coming from the right. This is opposite to what happened with the single nodes. Don’t you agree?
The last row shows what happens when the “natural direction” setting is activated. It only takes effect on the traffic_sign=* node. (It also does not affect any nodes on a way.)
IMHO, the behaviour with nodes on a single way should be exactly the opposite, to be in line with the very sensible default.
Maybe, to give people a choice, you could call the “natural direction” setting something like “switch behaviour around” and make it affect all possible situations.