Just a couple of comments:
1. Is it too much to ask people to avoid declaring "facts" about things they have not really checked out?
First of all I would definitely emphasise that Knoppix is a Live Linux and Klaus Knopper did not intend it to be installed as a full Linux install. You can do it but it will ultimately give you problems and the advice has always been to use Debian if you want to go this way.
I have said that several times myself in the past, and I don't think it is completely correct anymore. Furthermore, since the time of UNIONFS introduction, the borderline between a "full" Linux installation and a Knoppix Poor Man's Install is rather blurred. For example, I mount and use exactly the same volume with Java development tools in Knoppix as in plain Debian.

2. I think the best practice is to place the booting stuff in a partition that is normally only mounted during booting. That minimizes the chances for corruption, which should not be underestimated. In particular, I can't see how placing everything in a NTFS partition that is administered by Windows can be guaranteed to be completely safe, things may be changed e.g. with a new Service Pack. For example, on the machine I use right now, I run Knoppix off a FAT32 partition /dev/sda1, while booting is on an ext3 partition /dev/sda2 that is not normally mounted, and ordinary storage is on a large ext3 (or ext4) partition /dev/sda5 mounted on /store.