I use the double click to open my editor.

Keep remote..., can transfer unwanted files to the site.

Sounds like this would be a be a nice feature for a future release.

You can configure double-click to do transfer without confirmation. See documentation. Also you may find function Keep remote directory up to date useful.

How can I bypassing the Copy dialog window when doing a simple copy to/from my local and remote sites?

I do web design and like to test code on the website. Thus, I upload revisions many times a day. I know I can use my editor; but, prefer to do definitive transfers.

Al.........