Why can't you just use the sensor you have in a smartphone or in a simple hand-held camera with a microscope and get better quality more cheaply?
You're starting from a false premise — that the resolution tells you much about the image quality. The $6000 camera from your link has a 1/1.2"-format sensor, which has an area roughly 5× that in an iPhone. That larger area gives an inherent advantage.
As you note, this sensor is an industrial part, with very detailed specifications readily available; among other things, if you need that technical information for a paper, you're not guessing. And while it has different characteristics from sensors in typical consumer cameras, it is a high end part.
You can see more on what can matter in a sensor at What characteristics make a digital sensor good? — this alone is probably the key answer to your question.
But additionally, there are other distinguishing characteristics. For example, the sensor (and camera made around it) is available in a monochrome version, which means more per-pixel resolution if you don't care about color. And beyond image quality, the camera has features like gigabit ethernet output which are appropriate for a lab instrument; that
And, finally, the smartphone has a cheap lens built into it, a fixed limiting factor. This camera is an interchangeable lens system, making it much more versatile for whatever application.
Now, it may be possible that the consumer-device output will be just fine for what you need. In that case, awesome. But better quality more cheaply? No.