I normally rip the movie to the hard drive using AnyDVD as the decrypter. If I know in advance that I'm going to use DVDRebuilder, I just use the built-in ripper within AnyDVD and put the entire movie onto the hard drive and work from there. It is possible to work from the optical drive with AnyDVD in the background, but this is much slower during the encoding process and puts unnecessary wear and tear on the optical drive.
You can delete the EclPro folder if you want to, but it doesn't take much room. In the past, I used ProCoder exclusively with DVDRebuilder Pro, but my copy is a very old one, and I haven't used ProCoder much at all since going to Win 7.
Yes, DVDRebuilder works in both those operating systems.
By the way, I'm not sure if the free version of DVDRebuilder allows you to select movie only, if that is what you want. The way around that is to let AnyDVD do the decryption, then select the main movie only in DVDShrink and rip to the hard drive with NO compression. You'll get a warning message from Shrink that the movie won't fit, but ignore that. You can then work with the main movie only on the hard drive with DVDRebuilder to compress with highest possible quality.