For CC 1.0 bootmanager is installed on the memory card instead of on the CC flash mem. Bootmanager is practically the 'heart" of the chip. It contains all the configurations. Yes when you flash the firmware you can also install the Bootmanager.
As for the differences i don't know many but here's one from the CC website
I think the features are the same as the other Crystal Chips but i'm not 100% sure.
"HA" wire (not available on CC1.0 or any other chips in the market)
reduces the occurence of "mechacon crashes" which are the most
common cause of laser burnout in v12 consoles as well as reducing
the occurence of RSOD.
v7 PS2 w/ Modbo 745 (installed myself)
2x8MB Sony Memory Card
Network Adapter + 250GB HDD