The positions you posted are a nice demo of some of the algorithm’s behavior, yeah.
For now, dead stones affecting things is deliberate because a dead stone can affect eyespaces. Like, an eyespace with a weakness can be falsified by dead stones thrown in, even if those stones can be easily captured. The group having fewer eyes can affect things.
So in the case you posted, the way the algorithm parses it is that Black has a move to live in the first case of the empty bulky 5 (generally the way the heuristics try to break ties in unsettled positions is to rule in favor of living), and in the second case the dead white stone, even if it is supposed dead, is still sitting on the point black needs, therefore the algorithm still considers it to prevent two eyes just as a dead throw-in stone might falsify an eye.
Here’s another example:
The dead white stone, on the right, even though it really is dead, still means that all of black’s spaces on the right are false eyes and can’t become territory whereas on the left they could (if black plays first… or if both players are beginners and never see anything wrong with it black will even score the point at A5 too).
Ignore the black square right above the dead white stone - I didn’t actually expect that to be there when setting up this example! 
I should look into why it’s still counting a territory point there, it might be a bug. 