If u are working with playstation u can extract all the files u want from the iso even with winrar if i want and reinsert them with CD mage or isobuster (or was it magiciso??).
The only files u can't extract correctly like that are the .xa (normally audio), .str (normally video) or any file with video or audio inside.
The order of the files is relativelly important (isobuster will rebuild an iso with files in different order) so maybe it willl still work or maybe crash... depends on the game.
So the idea is usually to keep the files in the image, extract what u need from the iso (with cd mage or so) and reinsert it at the same place (with cd mage or so).
About TOC changer...no, it's not really the same as a repointer.
Almost all playstation cd have empty holes (empty sectors) between one file and the other and TOC changer allow u to change the TOC to use this empty holes and make the file(s) adiacent one to the other.
All this apply to all disc based systems, just check what sector size use the system and compare it will all type of data (raw data, audio and video). As example the saturn, it will have a session with raw data and normally more audio tracks after it. U need to work on the raw data and let the audio alone.