Motorola Droid X :: With Root Why Do We Need Custom Roms?

Please read this before you assume I'm an idiot Anyways, so my thinking is, we can root our Droid X. This gives us access to every system file. amirite? If that's the case, shouldn't it be possible to literally replace everything using some super user priviledged apk? I know linux well, and I know some android development stuff, but I don't know anything about custom roms (on android at least) and how efuse works, so I obviously could be completely off base here.The only hitch I see would be that while the phone is running, many many many of these files are likely in use. It just seems there would be some way to close everything (and I mean EVERYTHING), with the phone still running, and replace all system files with a new set.Now I'm not entirely savvy on how efuse works, and I'm even less sure on how changing the system this way would, from efuse's eyes, differ from a full custom rom flashing, and if, if it did work, you'd still be bricked on the next reboot.Thoughts? I mean it at least seems that we could find a way to replace motoBlur.