Poor coding skill accounts for perhaps 80% of the industry no-hires. Well...that's not exactly fair. Poor coding skill under pressure. Most Ph.D. candidates are either out of practice or used to taking a long time to think about and solve a coding problem. That's great for academic software, but misaligns with both rapid development and (importantly for the candidates) the style of interviews. Most Ph.D.s wither under the expectation of producing a feature very quickly.
Some Ph.D. engineers can code extremely well. If they don't end up at the company, it's because the following dialogue happened, implicitly or explicitly:
PhD - Look, I'm great.
Company - Yes, you are. How about $X?
PhD - Given my specialized skill, I was expecting more like $1.5X.
Company - Well, $.8X is what we pay the new grads, so $X is what we'll pay you.
In other words, their ability is clear, but their market value isn't enhanced very much by their specialization, when most companies are looking for the skills that developers get during their bachelor's or master's.