We already had this discussion, hadn't we? These are "copy protections", and not "play protections". It is the whole point, that they can be played, but not copied, isn't it?
From a technical point of view, a copier works differently than a player. At least CloneDVD does. These copy protections actually rely on this fact.
And it isn't only CloneDVD that fails, I believe other programs have problems as well.
AFAIK Shrink fails with DVD-ALPHA files from DVD Decrypter, DVD2One with Arccos rips. But they work without problems with AnyDVD.
You can take a very old version of CloneDVD1, from a time, where these protections didn't exist, and you can copy the newest protections using AnyDVD. You can't using DVDDecrypter.
Who do you think is at fault here?
I already told you, that CloneDVD will never get any code, which can bypass these protections for legal/political reasons. You could argue, "they are CSS protected anyway". Well, and if they aren't? CSS costs money per disc and is useless anyway. The "Puppetlock" discs I have seen were all not CSS protected. I don't remember, if Oldboy (ALPHA-DVD) was CSS protected, I don't think it is. No need for DVD Decrypter, but if CloneDVD copies them right away, it would be illegal in Germany. (They sell CloneDVD in big stores there, you can buy it from amazon.de, I hope you get the point).
If you claim to support these new protections, you should start to deal with them properly first.
What you currently do is misleading. Putting "files on the harddisk" is probably good enough from your point of view, "but that's not really for the good of the public". They want to use the tool of their choice to post process them.