Yeah I thought about that as well after posting, they would/should definitely be separate. Not only from the technical limitations, but to protect the user from being banned off the PSN as well. Because upon connecting to the PSN Sony would know what programs are on the system, and if there was any homebrew on the updated FW boot, the risk of getting banned would be great.
Although I'm sure if this was done Sony would quickly patch in a fix or do something to sabotage the CFW boot so the user would get stuck in the current FW as soon as they upgraded again. Or at the very least Sony would modify their next FW to poke into the other partitions of the PS3 to search for CFW/homebrew so they could ban the user off the PSN.
But still, would be pretty neat to see this get developed.