How would you go about extracting/importing files using standard CD image tools if the TOC is invalid?
Well, you simply ignore the TOC descriptors and don't rely on generic tools. Think of games like Chrono Cross which don't have any ISO9660 file entries. You can still extract and insert them fine, even if there's no name anywhere to be found.
Does it not make sense to keep the files readily accessible. The modder would need to maintain the internal LBAs and filesizes.
More like the tools doing that part of the job for you. Maintaining most of the stuff manually (if not all of it) is rather tedious and error prone.
But the files would still be visible to general purpose tools. Not just dumped somewhere in the image and out of reach.
Considering most tools used for this are supposed to work in both read and write modes (unless we're talking about simple viewers), the image entries become quickly useless and it's better if you simply keep using copies stored on a different drive, like an external hard disk. The ISO itself should only be kept for insertion and testing, at least in my opinion. And anyway, even if you kill the TOC descriptors entirely you can still rely on the real information used by the game to access said data, so nothing is really lost in the end other than a few names.