ABGX can insert few missing files (what eveyone call "Stealth" files) in case the ISO don't have it, to make the game exactly as the original game in a ISO, actually the current ripper FW (firmware used to convert retail games to ISO's) do all this job extract and insert these missing files so you don't have to worry about it anymore. Older ripper FW's used to copy only the ISO file to the computer missing these files and we had to insert them manually that why happened so many bans in the past because most of people didn't know how to patch them correctly.
Now, ABGX is used to verify the ISO to see IF match with the one that is on their database, as said above all you have to worry if everything is Green, this means it matches with the one on their database and is a complete copy of the game. if has Yellow, it will work but it doesn't match with their database or they don't have it yet, they usually add it after the game is officially out. if not they might no have this version or just it never was a final product, so is up to you if burn it or download from another release/scene group. AND finally if has Red, it have any corruption or the topology data is missing, that might be or not fixed, just run it on level 3 trough ABGX.