There is another advantage of using a locked down file system --- you may not be able to use a rootkit to break root and then modify the file system, but some unfriendly adversary, such as the FBI or the NSA, won't be able to do it to your phone without your knowledge, either. I would think that's worth the inconvenience of making sure you buy a phone with an unlockable bootloader. (Since unlocking the phone requires a wipe of the disk, you don't have to worry about the FBI/NSA doing this to access your data on the phone without your knowledge.)