I don't know if they've addressed it. But ~15 years ago, my father was mentoring some college students and noticed that while they had been taught to machine a block (i.e., the rudiments of machining), they had no idea how to design appropriate tolerances for e.g., a gear because they hadn't ever made anything that complicated. So it was an issue back then. Presumably these details are learned on the job through trial and error, or by oversight from a more senior engineer who understands the requirements better. But in the past it was understood you'd start learning them from actually building parts as part of the curriculum.

Doesn’t matter, if you ask for physically impossible features to cut this is something you could technically do. Or you ask for a feature that adds multiple setups to an otherwise simple part and makes it wildly expensive

The CNC doesn't know either. What usually happens is that an engineer at the CNC shop figures it out for you.

Knowing some machining still lets you design parts and assemblies that are some combination of cheaper, better, etc. This is noticeable with precision or high performance assemblies. And how many revisions are needed.

Lathe, mill, CNC, or matter transmuter, doesn't matter. Effective design only becomes possible with intimate knowledge of how it is built.