Good point. Because only small Macs should run from CF cards. I understand where you're coming from, but CF cards have more virtues than their small, quiet nature.
The problem with those $1 / 1 Gig drives is that their longevity and flexibility are both issues. The drive I have in there now is one of only three remaining from a lot of 7 that I bought - the other four failed - one head crash, two cases of stiction (which yes, I know could be fixed), and one dead controller board. Further, I plan on using this Quadra to run some Max patches, and it will be traveling occasionally, Without moving parts, CF cards should hold up much better than old hard drives. Further adding files onto a CF card is a piece of cake with a Macbook and an USB-CF reader.
So, it doesn't look like anyone regularly boots different systems off of different partitions. Good to know... maybe system picker is the best route. If anyone does happen to have a CD of HDT 2.0.x they'd be willing to part with or image, let me know.
Thanks!