Making a machine CNC ready has a neglible cost. Electronics cost nearly nothing, and are easy to do when your not aiming to super quality. All of the moving elements can be simplified because you dont need to present user interface through mechanical couplings and dont need to worry about user safety.
So a bit counter intuitively cnc machine can be simpler ...
The two existing comments are correct IMO, it's mostly due to economics. The price to produce comparable CNC and manual machines might be close, but the demand for CNC's is much greater than manual machines.
Every shop I've ever been in, from mom & pop places to 1,000+ employees, has been 95% CNC with manual machines reserved for tool & die making or ...
The "three plate" method has been used as the basis for precision manufacturing/inspection. This
is a decent summary, it's pretty ingenious and only requires dye and abrasives.
This will teach you everything you need to know and then some, "Foundations of Mechanical Accuracy".
there is a whole genre of "square block" videos on YouTube by various machinists. The standard tool seems to be the lathe.
But really, you are asking how to set up a machine to be perpendicular.
apropos, video for your edumatainment