Overwrite confirmation does not work in the first seconds after changing directory
In the Commander interface, use the local pane to change directory, then RAPIDLY drag and drop a file already present in remote from local to remote panel: no overwrite confirmation is asked, the file simply gets overwritten in remote dir.
Note that if you wait some time, letting WinSCP "get aware" that the remote panel has changed directory as per synchronized browsing, then the overwrite confirmation warning correctly appears.
So this seems a sort of timing issue, when the local panel doesn't wait for the remote one to be ready when checking if the file that is being dropped is present in remote.