I am by all means no expert with how PS3 works under the hood. That being said, the PS3 is still heavily utilizing the core OS, kernel, and configurations written for the original PS3. These CFW teams (really just
@Evilnat at this point w/ the help from various people across this site) have just added layers of customization on top of the original build and various modifications to existing files.
Most modern OS's still require a reboot to install software updates, and in many cases will boot into another partition while it installs critical files that cannot be written when the kernel is in use. PS3 does this when installing via PUP files so that the critical files are not in use when they are updated and utilizes Sony's built in update system.
If you want a CFW that no longer relies on Sony's PUP update system, something would need to be written from scratch (I assume), and I don't think that interests anyone or would be beneficial.
Some of the smaller 4.91.2 Beta changes that were being put into place were simple modifications that could be written without requiring the entire OS be re-written to flash memory, which is why
@aldostools tried to capture these in webMAN Mod as updates that don't require an entire flash (some of the updates included patches to the critical underlying files so those specific Beta patches had to be installed via the PUP regardless). Not sure if Aldo continues to plan on supporting that update model with 4.91.3 Betas but I for one would welcome him to continue so I don't have to fully flash my PS3 for every incremental update. IIRC PS3's have a limited number of flashes for these chips before they stop working / create bad sectors.
Long Story Short, EvilNat could figure out a different way to publish some of the smaller changes outside of PUP if he wanted to, but eventually the CFW will probably need to write critical files for changes he is working on so I assume he would rather make sure PUP is working with each released Beta.
If anyone is more knowledgeable than me with the underlying PS3 kernel, OS or hardware, feel free to revise and correct any of my assumptions above.