What I'm not aware of is whether using clonedvd to process a video_ts folder that was dragged and dropped off the original disc onto, say, your desktop will produce the exact same result as using clonedvd to rip from the original disc (especially heavily protected discs). And that's what Supergoof is asking; I don't believe the question has anything to do with Clonecd.
Thank you both for very interesting discussion.
You understood my question correct. When I was saying "1:1 copy" I did not mean bit by bit copy. I meant functionaly equivalent copy: with all menus, titles, audio and subtitle tracks and so on. I don't care about layer break either (thought information about it should be in one of .IFO files as far as understand, at least after grag and drop).
Currently I play my DVDs with "Mediagate MG-350HD" multimedia player connected to my home network. I shared DVD drive on my laptop, and when AnyDVD is enabled, "Mediagate" is able to play VIDEO_TS folder on that network share. It upscales to 1080i too. Also I can select NTSC/PAL (which at 1080i means 60/50Hz) depending on disc.
Yesterday I bought "Pursuit of Happyness" and "DejaVu" Region 4 DVDs, and "Mediagate" seems to play them just fine. So if I copy them to hard drive, it will not make any difference, I assume.