There is always some risk that refactoring makes code not only different, but worse. Corner-cases are often there for a reason, and refactoring sometimes misses them, especially when there isn't complete unit test coverage. Since it's often easier to get the core logic right, this likely leads to issues that are discovered in production.
A good boss knows to get out of the way, clear a path if necessary.
If boss can't trust the minions to do the right thing, someone's got the wrong job.
There are many people who have wrong jobs.
More importantly, there are many people who are good, but not perfect. They do some aspects of their work greatly, other aspect less well. Good boss has some idea about that and is able to work with people who are not super great.
Least not last, even very good people often disagree about many things, including whether refactoring is needed or not or what kind of refactoring to do. Even if boss trusted all and listened all, he would still be told plenty of contradictory opinions.