Hi, Darkside. Let's see if I can shine a little light.
1) I'd have to go hunting for this again -- it's been a while since the initial research -- but in general we're excluding each item suggested by Apple. These are all either temporary files or system-regenerated items that aren't valid on a different volume (or, potentially, machine). There's nothing here that is "dangerous" to exclude -- we're very careful.
2) Desktop DB/DF is a bit of a special case. OS9 people were having problems when backing up to a drive that had a different name, and were often forced to rebuild their desktop. Removing these files causes an 'automatic' desktop rebuild, which ensures things are correct when booting from the clone (but it does extract a one-time time penalty).
3) Unless this is a bug, there's no doubt some arcane reason why we did this that I can't remember (or think of) at the moment. My brain has turned to mint jelly after the last week or two due to the increased level of support traffic generated by Tiger's release. I'll look into the reasons again and, if appropriate, make a correction in a future release. Thanks for the question.
Thanks for the kind words about the UI: I'll be writing more
blog posts about the genesis of SuperDuper! and its UI (and v2.0) in the coming weeks, so stay tuned!