During the peer-review process, you modify the manuscript until the editor accepts it (who in turn consults the reviewers for their opinion as needed).
This applies to the entire manuscript, including the title.
The latter may very well change due to the reviewers’ recommendations, in particular terminology is often changed in my experience.
Thus, explicitly asking the editor-in-chief for permission to change your title seems overkill to me.
You don’t have to do it for the same reason that you do not have to ask for explicit permission for every other change of the manuscript.
That being said, a change in the title can easily be overseen, even if a diff is employed.
Therefore I would recommend to simply mention the change of the title where appropriate in your resubmission, but without being overly submissive, e.g., like this:
Please note that we changed the manuscript’s title to […], because […]
We followed the reviewer’s suggestion and now speak of gorgleflorps instead of florplegorgs whenever appropriate, including the title.