CSS Display defines atomic inline as

An inline-level box that is replaced or that establishes a new formatting context

An element with display: ruby has the inline outer display role, so

The element generates an inline-level box.

, and has the ruby inner display layout model, so

The element generates a principal ruby container box, and establishes a ruby formatting context.

Therefore, display: ruby should produce an atomic inline box according to CSS Display.

However, CSS Ruby explicitly says otherwise:

Ruby containers are non-atomic inline-level boxes.