So if I've got the right idea, the clearances harder to achieve for a fan vs a lego piece because you're not just concerned with the static tolerances of the shape of the fan, but also the dynamic forces that will make the blades flex and bend under load.

Clearance in this case is how far away the blades have to be at rest, such that the dynamic forces the blades experience under load won't flex them outwards to the point they scrape against the enclosure. Which I'd assume has far more to do with material properties than it does the raw geometry of the blade.

Now I wish I had a high-speed camera to be able to inspect the dynamic deformation of a noctua fan. I'm curious about how rigidly they behave under load.

0.5mm is the clearance, not the tolerance. Tolerance must be significantly smaller than clearance.