I don’t work for iXsystems so I don’t know what drove the adoption of the Atom board across the product line. The older line used an AsRock Rack C2750D4I from Mini to the MiniXL, the latest lineup includes multiple motherboard choices (chosen from the same C3xxx SuperMicro motherboard family).
Can more performant systems be built in a Mini form factor? Sure! We recently had a discussion on this topic. The AsRock Rack X570D4I-2T Ryzen motherboard mentioned in that thread can run circles around the C3xxx embedded processors in the current Minis - but you’d likely need a better ventilated case depending on what Ryzen CPU is put in there.
Rolling your own system, you’d also lack the excellent support that iXsystems provides its customers. Whereas AsRock Rack B2C support can only be described as uneven, iXsystems customer support outshines even SuperMicro.
I was so glad to have iXsystems in my foxhole when the C2xxx series AVR54 bug hit the industry because they worked through multiple C2750D4I board replacement iterations until I ended up with a v1.3 revision warranty replacement that works to this day.
So, can you build more performant Mini-ITX boards? Sure. But that is not why people should buy the Mini in the first place - it is meant as a file server that quietly performs its duties while giving admins a platform to explore TrueNAS with.
I “graduated” to a different motherboard and case not because I wanted to but because iXsystems didn’t sell it. My use case and preferences are different than those of many customers, so I’m very grateful that iXsystems allows me to run their software on my current hardware rig.