there are no dummy files.
look, the problem starts with the dynamics of the wheel. when the disc spins, the tracks near the outside edge are actually moving over the lazer eye several times faster than the inner tracks, because of the length of the tracks, it's longer around the outside than near the center, so there are certain files that should'nt bee to close to the center, and the software for mastering ps2 discs lets you fix files to any lba adress you want. I made a dvd cogwapper, files on which totaled some 300kb, not much there at all, but by fixing those to an lba near the end of the disc, I build and iso over 4gb, the size of the iso being equal to the TOC, which is based on start to end, not on the size of the files. The empty space forced by fixing the lba is counted in start to end disc images, but they zip to 300kb becuase the compression software knows theres no data in between, and packs just the files and notes where they'll go when it unpacks out over 4gb....of nothing, really.
If you MUST rid yourself of that space, and you can for playing from hd, since they do that to them for ease of disc read that doesnt apply since they arent on the discs anymore, you'll have to remaster (the files on) them with the Sony CD DVD Generator app, and iml2iso, which makes an iso from the save project ".iml" files saved with that, into burnable iso's, the way I make all my homebrew and remasters, since the developers debugging consoels I use don't support ps2 cd-r's, to mine ALL cd-r's are PSX discs, so I make everything into dvd's, which is a lot cheaper, free, in fact, since I upgraded the lazers, and I can use re-recordable dvd-rw's for "trial and error", until I get it right, before I burn the final working version on permanent media, I know it's right.
A toxic agent on a dangerous mission so secret, even I don't know what it is, because if I did, I would have to kill myself. I don't even know who's side I am on.