I wouldn't think it will be long before someone writes a new backup manager that allows for split files (e.g. File.001, File.002) which would be a very quick and easy solution to the 4gb limit.
It would be extremely difficult to change the way the game works by splitting the files. It's the reason why the wii has wbfs; It is much easier to write a simple file system and have a program that can access it.
The way the wii did it was basically a fat system without the 4gb limit. Notice how, even to this day there is no ntfs support on the wii. Its because its hard to implement. EXT2 or 3 would be easier but then you have to deal with the 12 yr old script kiddies whining that it won't work in windows. (yes I know there are programs to make them work but not for win7 AFAIK)
My opinion, make a program similar to what the wii has (if not identical considering its open source) and make a psfs partition that works. Simple, easy, and probably the fastest fix.
i'm going to order this board, i believe even if Mathieulh won't release anything a similar solution will be available in the future! but i bet he will release his documents, considering that this whole psjailbreak thing won't be a secret and other hackers will clone it and share with us the free solution.
Mathieulh won't risk losing the fame, i bet my money on this!