Good questions, Gregory. I’m still learning this stuff as I go and often forget and have to re-learn it.
Pixel size and sensor size both affect overall image quality. Here’s a good article that explains pixel size better than me, which also links to a follow-up article on sensor size.
The short answer is that the Blackfly is a big upgrade.
Firstly, we can look at price as a good indication. Both are mass-produced and have competitors so we can assume the price is fairly reasonable compared to other cameras that are similar. The RPi HQ is ~$25USD and the Blackfly is ~$450USD.
What are you getting for this big price difference? Image quality. This brings us back to image size and pixel size.
The Blackfly’s overal sensor size is much bigger than the RPi camera. Although its overall pixel count is lower, you’re getting a wider sensor area which means a lot more light. This means you’re going to get a lot more detail, especially in the darks of your image.
To put it another way, on the RPi sensor, you have more pixels collecting less information, and on the Blackfly you’re getting less pixels collecting more information. The resolution on the Blackfly is still 3072 x 2048 which is 2x standard HD, so you should be good there for print. Of course, if you’re cropping your scanned images in post, you lose some of that so fill up the field of view with as much of the final image as you can to take advantage of the full resolution.
Another important spec to look at is dynamic range, which is the number of “steps” between pure black and pure white the sensor can capture. A good comparison is “t-stops” in regular photography. A lens with 2.8-12 has less dynamic range than an equal lens with 2.8-16. The measurement for dynamic range is “db,” short for decibels. The higher the number, the better the dynamic range.
The RPi cam specifications on this are a little vague, quoting “67db @ 8x gain.” Taking a look at this chart on Wikipedia, we can see that this is equivalent to about 23 stops, which sounds great until you add in the “8x gain” part. Gain is an electrical adjustment to the pixel readings which artificially enhances the range. The result is visual noise. Usually lots of it. The actual dynamic range of the HQ camera (according to some well documented tests) is about 11.3 stops. The Blackfly, on the other hand, as a db rating of 47, which is equal to ~15 stops. This doesn’t sound like a big difference, but remember that each “stop” is twice as much light as the previous one. So you’re getting almost twice as much light into the Blackfly.
Lastly it should be noted that some people report having a hard time getting the RPi cam to give them actual raw images without compressing or altering them before spitting them out. If you search these forums you’ll find a few threads on that.
TL;DR - Blackfly is getting more light to a bigger sensor with more sensitive pixels. You’ll be getting a lot more visual information and that will make your work in post much much easier.
If any of that is confusion, please let me know and I will try to clarify as much as I can.