Exactly? I wasn't the one who classified Drew Barry's work, widely acknowledged as some of the very best and most accurate in molecular animation, as "lies" ... so, not really sure what you're saying? In reality, humans can't see down to the nanoscale with their eyes, yet there are real 3D structures down there that have a physical form. If we display them as being a couple of inches large so that humans can see the shape, is that misleading? Should we never try to visualize anything for fear of it not accurately representing reality?
I guess my point is, as someone who has done a ton of work in this area, there are a million choices one can make when choosing what to visualize, and the lines between truth/reality/lies/accuracy can get muddled. A lot of it depends on context, use cases etc. For example, a star high school teacher may show one of Drew Barry's animations to their class and use it as an example of the limitations of visualization. A creationist could use the same animation as evidence of "God's perfect design".
What I'm understanding from the article and from your arguments, is that unless you can guarantee that a piece of work 100% represents reality in all its complexity, it does more harm than good. I'm politely disagreeing, I think it's better for these works to exist: "Perfection is the enemy of done".