I agree that feature flags can be a solution sometimes. The presentation and the paper I linked to in my question discusses this, but they also mention large-scale refactorings and this is where I don't see how feature flags can help.

For example: How do they untangle a wad of code that is large enough that it takes longer than a few days and more than a single developer to get the code back into a state that is acceptable for trunk?

The changes required for this kind of refactorings can be all over the place, regardless of any organizational boundaries in your code. I can't see how changes of this nature can be put behind feature flags.