For games such as START OCEAN where the file names are the same for each disc (meaning that overwriting/skipping file copy is not good) , I have an idea.
There are probably some files that are 100% the same regarding data, then there are the files that have the same names, but have totally different data. Data such as levels, cutscenes, etc.
So how would one differentiate between the two? Well the files with the same data are small, and the files with different data, but same name are huge or they have an important name that same it appear to be a cut scene, etc.
A possible solution would be to combine the files that are huge (appear to be movies/level/etc) and not combine the files that are small ( or don't appear to be movies/level/etc).
Step 1: Extract all the discs into separate folders (Disc 1, Disc 2, Disc3, Disc#...).
Step 2: Add a numerical value to the huge/level/movie/etc data files in correspondence to the disc. For example for a file named "level.xex" in the Disc one folder should be named "level1.xex", then for the same file in the Disc 2 folder should be named "level2" and so forth
Step 3: Combine all the files into one folder while still following the folder structure tree. The files will a numerical value will not overwrite each other and the files with the same name will be overwritten. So basically take all the files in the Disc 1 folder and cut/paste them into the Disc 2 folder, and click yes on overwrite all.
Step4: Open up the Windows Command Prompt (Start->Run->CMD) and for each folder with files that have a numerical order, go to those directories in CMD and run the combine files command. For example a folder that has the files: "level1.xex, level2.xex, level3.xex" run with command: copy /b level1.xex + level2.xex + level3.xex level.xex
This will combine all the files into one file. Then you can delete the files that are in numerical order.
Step5: Play the game.
This probably will not work (or will it), but this would be the first step to figuring out how to make it work.
If there were some program available that could open up the proprietary archive files, then the files inside could be combined into one container file.