So, to summarize ... you can re-rip the DVD in "file mode" with DVD Decrupter and then you'll have the "video_ts" folder you were expecting.
Or, you can use ISO Buster or a similar tool to extract the "video_ts" folder from the .iso file you created. This might be faster if your system can copy from one hard drive to another faster than it can rip data from a disk.
Usually, I only use DVD Decrypter's "ISO READ" mode when the source disk is a DVD-5 and no compression or reauthoring will be needed ... then I burn the copy with "ISO Write" mode. Be sure to select the ".mds" file as the one to burn. The .mds file tells DVDD how to write the ISO (disk image) to the new disk... Some people can get away with selecting the ISO itself, but I had problems doing that.