I am in the process of finishing up a PhD (Robotics, Cornell) and spent some time looking for jobs outside academia. What you write sounds very familiar because I heard it almost everywhere I looked. There seems to be a widespread misconception that graduate school consists of people focusing on one (usually obscure) topic without ever doing anything that "normal people" would do in a "normal job".

Here's how grad school really works.

At least in the US, completing a PhD requires you to take classes. I took classes in my field (Mechanical Engineering) and in my elected minor field (CS). None of them had anything to do with my research are (modular robotics): Vibrations, Linear Systems, Feedback Control, Intermediate Dynamics, Intro to AI, 3D Perception, Evolutionary Methods, Autonomous Mobile Robots (you get the idea, there are more). I also took a management class and a course on technology commercialization, but that's just me. Basically, they are the same classes Master level students take (and companies pay them a premium for doing so), just more of them.

Very few grad students work on only one project during their PhD program. Many students "bounce around" for a while before selecting an adviser. Sometimes projects don't work out and you switch to something else (happened to me). Sometimes the availability of grants dictates what you are working on and when. And often you just start a new project because the old one is completed. What causes every PhD to have that brief, often obscure sounding, description for their work, is that the thesis describing all those different projects needs one title (not five). When you open the cover of the thesis you might find sections on a wide range of topics covering many areas of expertise that the author had to master before being able to produce original work in their obscure topic area.

There might be disciplines where you can work exclusively on one subject area without using any external tools. I don't know any. As a PhD student you rarely have someone to delegate work to. And because what you do in a PhD is new, you often have to build your own equipment for doing it. As a result of having to do everything yourself, you often end up accumulating experience of varying depth in all kinds of languages and technologies during grad school. Dealing with external suppliers and contract manufacturers is also quite common, at least in engineering. My actual everyday work in grad school is definitely more varied than any job in any of the companies I have seen.

Soft skills are something frequently cited as an area that PhDs are lacking in. I don't agree with this assessment. Some skills are less important in academia (negotiation skills, leadership), but others are more important (endurance, teaching/presentation skills, ability to learn quickly). Only very few scientists are the socially awkward eggheads that popular media portrait them as.

Finally, it's worth pointing out that PhDs have spent several years working in the future. The technology that in development at universities today includes things you might consider cutting edge a few years from now. Your freshly graduate PhD job applicant just spent five years interacting with this stuff and the people building it on a daily basis. If your company can't make use of having somebody from the future work for you, I'd consider that a problem.

Please do yourself (and people like me) a favor and kindly stop pigeon-holing anyone with a PhD as "overspecialized". Have a look at what kind of work they were doing during their five year time in the ivory tower, and see what useful skills they needed to get their maybe-not-so-useful research done. You might be surprised at the breadth. And don't worry if your PhD job applicant's qualifications are a little strange and don't quite fit between any of the department walls in your company. The PhD is used to working interdisciplinary and learning new skills quickly.