What is the atomic unit that makes up a Cover house and how does the company facilitate mass customizability on the hardware side of the business?

You need to have that underlying unit, else you aren’t building a product. It's a service. And services don't really scale, even with software. 

We make these building blocks — standardized sets of wall, floor, ceiling, and window panels—that connect in a standardized way. This limited set of pre-designed, pre-engineered panels can be used to create an infinite number of different floor plans. While it’s limited customization, it's extremely versatile. This is comparable to what you would get with conventional construction in terms of layout versatility.