The modded eboot is the original one but with some codes injected to it
If you install any pkg, the game will start reading from the pkg which means if you put a a modded eboot in the game ISO the cheats will work & if u install an official update pkg the game will stop booting from the modded eboot & starts booting from the official update.
as for the PS3_EXTRA folder just convert it with the other folders to ISO normally the ISO should contain these folders:
PS3_DISC.SFB this one is a file
in your case just put it like these & the PS3_EXTRA included so it will be like this:
& for borderlands convert both folders.