Yes. That is the Open With feature. It works as it is designed to. Allowing people to use their favorite html editor instead of Sigil's to edit their epub's html; or allowing them to edit/resize their epub's images with their favorite image editor. All without having to deal with the overhead of exporting/editing/reimporting (or unzipping/editing/rezipping/reopening).
I'm a little confused as to why you would be surprised that Sigil updates immediately when you click "Save" after making changes in the external editor, though. I would think that after taking the time to make/save changes, one would want/expect to
see the changes one made after saving. A warning that saving changes to a file is going to result in changes to a file would seem like overkill to me.
P.S. I'm not going to delete any posts. The Open With feature and external editors and their behavior are at the very least tangentially relevant to what the OP is talking about.