What I mean is that a big refactor might take 9 months to do atomically whereas it could have been done in 3 months as a massive single PR. However I guarantee you we'd have spent 6+ months cleaning up unexpected issues that show up after merging the giant PR. In the atomic commit approach what you get at the end of the 9 months is a solidly engineered product without those issues.
I will say that on a team, issues that you encounter are that it is very hard to keep track of these work-in-progress refactors that are getting in piece by piece, and it can cause rebase hell for other committers if there is a lot of refactoring involved. Splitting one giant refactor into 3 smaller refactors is better for the product, but represents 3x the work for other team members who have to rebase all their changes every time something is merged.