Thanks for your suggestion.
We will see, if more people ask for this.

Though note that you can use either synchronization:
https://winscp.net/eng/docs/task_synchronize_full
or New and updated files only transfer option:
https://winscp.net/eng/docs/ui_transfer_custom

In the overwrite file dialog provide an option to choose YES or No for "same only".
This way the dialog will only pop-up on different files, allowing to concentrate on the differences.