Maybe it was that the manager was being pressured to PIP a certain percentage of people, and instead pushed back really hard to retain this person because they wanted to retain them instead. Before spending their political capital, they asked the employee if they were committed to the long haul.

In the end, they went to bat for the author and then ended up in the same place. They could have just PIP'd them with a lot less effort.

The article doesn't make the reason clear, but this seems more likely to me than vesting stock.