Even the phrase "hand-built" doesn't necessarily mean what people think. For example, as of a few years ago ALL Shimano wheels were hand-built.
A look inside Shimano's shrouded wheel factory | Cyclingnews.com

Here's a recent example from DT Swiss.

To a large extent, wheel quality comes down to time & effort. Steps like stress reliving and re-tensioning take more time than a simple load and tighten. Ultimately, a personal custom wheel builder is more likely to be able to cope with variation. For example, "does this rider need less tension because they're light?". Assembly line factory wheels have the advantage of starting higher quality consistent parts. There's no mailing parts across the country and then discovering that the rim is a hair bent, out of spec rims would simply be binned.

Both approaches can produce excellent and reliable wheels. Factory wheels generally have access to features that a custom builder won't (for compatibility). Custom builds can give you a wheelset perfectly suited to an individual's riding style.