Meh, he was still right. Nobody really does care - it's just a cool visual more than anything, and Dark Water is such a masterpiece episode as it is that I couldn't seriously ask for any changes. Of course it doesn't make actual sense - no Doctor Who story does, including all the ones you mentioned. If you want to approach them with a rigid imagination that can't fill in the gaps between the cool concepts and emotional moments, then that's fine, but there's no real issues in this instance. Every problem you can raise can just as easily be explained with a few second's thought - dark water isn't actually water, for instance, so it's pretty safe to assume 3W marketed it as some way of nulling the feeling of the dead. Perhaps by limiting the after-feeling to just the skeleton. I won't argue that a few extra lines of dialogue could have cleared all that up, but I also think that anyone who needs those extra lines of dialogue to appreciate the brilliance of that piece of television should probably try a less overtly nonsensical show than this.