Yes, case in point, I got to know about this paper through a fellow academic who left academia a few years back. He could not reach the top. He hence has a clearer view of what is wrong and how it disadvantaged him in securing a permanent position in academia. Yet, he's likely a better scientist, both in coding and physics, than many people that I know at the top.

We're trying to move to a more open-source approach in the lab I am in now. The problem that I see in our case is that academics are notoriously messy and lack proper documentation of code. Also, time. Why would one bother doing this extra work when so much is already asked outside of actual research?

The whole system needs to change. There are fundamental flaws that make it extremely hard to change things, even incrementally.