Every PR is a single commit. The only extra commits on a PR would be "Review feedback", etc. But it would be squash merge and the final commit message updated to include any important details related to the changes from the feedback.
Consider the case from the article. refactor: 25, api: 500, migration: 50. Lets say 25 = 1 day of work so we have refactor: 1 day, api: 20 days, migration: 2 days. I'll decrease api to 5 days (1 week) for simplification. You pick up the task on Monday and do the refactor. Now, you have 5 days of work ahead of you on the api. Don't you feel you are looking over your back hoping no one on your team touches those lines? And then on day 5 someone does the refactor but slightly different. You have a commit so you have to do some rebase magic when you catch up to master. No thank you. And you doubled the work, your coworker wouldn't have had to do it if you had checked it in 5 days ago.
Consider a deadline. Consider a major production bug in the api that you discover when you release it. In my plan, you end up releasing the api early so you catch the bug early. You can petition for more resources to fix the problem since you have extra days which were reserved for the migrarion. If you try a big-bang release you find the api bug later, decreasing the likelihood that you can fix it within the deadline. I think of amortizing the risk of my releases across time rather than allowing the risk to accrue.
I could continue to defend this with more examples but the real fact is there is a tradeoff here like tabs vs. spaces or emacs vs. vim. But that tradeoff is ship fast vs. reduce interruptions for developers. Because creating a PR, reviewing a PR and releasing a change are interruptions for developers. And some developers will find ways to reduce interruptions. I have my preference for shipping fast for the reasons above and my experiences between cultures that result from the choice of prioritization in the tradeoff.