Restructure ApplyBoundaryCorrections and support AtomicBoundaryInbox

[nilsdeppe]

Proposed changes

I'll need to squash the two commits later, but I figured this is a bit easier to review.

Upgrade instructions

Code review checklist

• [ ] The code is documented and the documentation renders correctly. Run make doc to generate the documentation locally into BUILD_DIR/docs/html. Then open index.html.
• [ ] The code follows the stylistic and code quality guidelines listed in the code review guide.
• [ ] The PR lists upgrade instructions and is labeled bugfix or new feature if appropriate.

Further comments

[nilsdeppe]

@wthrowe this is ready for you to look at again

[nilsdeppe]

I've rebased and squashed in the couple changes. Sorry for accidentally dropping that comment!