Package management is a valid reason, I agree, but it's possible to use package management on the front end, too.
A package manager can provide a manifest list of files associated with a package. Filtering copy-all through such a list isn't hard.
I have no problem with warnings, but the installer might want to prepare the user in advance to know he isn't getting a broken installation. The fact that the program actually completes execution is not (as a rule) the way to tell whether something was done badly during a run. Yes, lots of scripts I have seen send error messages 2>/dev/null because the author knows the warnings are essentially bogus when he writes the script.
Still all in all I think grml2hd is nice work. I do appreciate the de-select services dialog, thanks.
Mark