Alex,
The cold hard reality is this.
Yes, you can replace the firmware on a Sony using a program to pull new firmware off a memory card into RAM and then program it into the FLASH. But, and you knew there had to be a but... if that image made the Sony un-bootable: you're toast. The tool requires the Sony to be able to run a program to do this, so if it can't get back to the point of running that program... you won't be able to fix what you broke. Only Sony could fix it at that point.
The first filesystem supplied with the tool could hack the Sony to eliminate the signature for using the USB firmware method. But I can only imagine Sony would then close the door for the memory card based tool, upgrade off SHA-1 signatures and provide a fixed PDF viewer and some other nifty feature everyone would want to get most users on the newer even more secure firmware. Or just simply show their ugly and upgrade the DRM and tell everyone: upgrade by this date or you can't buy new ebooks from the CONNECT store.
Even with a working firmware upload ability, as with the original firmware, uploading entire filesystems to add a tool will rapidly become a mess: "I want the Mobipocket Viewer but there isn't an image online with that and the Go game"... if creating Sony Reader filesystem images was easy for your Average Joe they'd be making them already to add fonts et al.
On the silver lining side of all this, the things that make 3rd party apps a bust on the Sony are the same things that make the unit more solid and robust.
