It protects against the accumulation of small variations that create big assembly failures. Typical failures include interference where you expected clearance, a lost clamp due to a short stack, misalignment that causes binding, and a mismatch that forces hand-fitting. Stack-up is how you prevent “works in CAD, fails in assembly.”
Avoid deep, narrow pockets that force long tools and chatter.
Control datums that match how the part will be fixtured.
Add realistic internal radii rather than sharp corners.