I think this all makes perfect sense and seems like a good starting point.
I would second Pablo’s comment above that building a framework that all the different features hang off of makes sense, and that dovetails in what what you’re suggesting about a “kernel” at the core of everything.
Making almost everything a kind of plug-in module makes a lot of sense here, because of the wide variety of cameras, camera interfaces, camera drivers, home-grown LED setups, Motion controllers (Arduino, Raspberry Pi, ClearCore), sensors, etc. It also leaves open the door for software-only add-ons, like scopes, or even post-scan processing steps like file format conversions.
With this kind of setup, you could basically choose the modules you want to include in your scanner and make it as simple or complex as you need.
The main thing with this kind of setup is really getting a very well thought out, lightweight, simple framework that’s flexible enough to handle all these different kinds of modules.