It's definitely the case that a mega monorepo doesn't, in practice, have the atomic commit property. E.g. once you add owner files and separate code reviews, you're in for a world of hurt. Case in point, Google developed an internal tool to split cross-cutting CLs into manageable pieces, wrangle all the owners and approvals, presubmits, etc, and then submit the CL piecemeal--i.e. not atomic.
Chromium uses a different model. It just DEPS's in other repos at pinned versions. That has a whole other set of problems.