Yeah, it is a 3 second pregap on most NEC discs when it comes to transitioning from an audio track to a data track, but it's a special kind of gap, some sectors marked as audio, some as data, etc. Whatever the reason, that program failed to detect that properly. It could still burn a working CD-R with proper offsets though. The offsets for every track were taken from the original CD's TOC, and that's not how hard to read or process, so I don't think it failed there.
The thing about TurboRip is it that I created it in preparation for dubbing Ys IV (or anything else) and to make it easier to patch CD games in general (Xak III included). I had 2 CD RPG games that I fan-translated and I needed something just like it to rip them in a certain way, track by track, to ultimately produce an ISO/WAV/CUE image file set and to do it correctly. Got tired of all the problems in patching with BIN/CUE rips and I had the motivation in '06 to do this. Anyway, you don't need the images in ISO/WAV/CUE form per se, unless you wanna say archive them with a lossless encoder like APE for backup purposes.
To the point, what is your goal here ? If it's just to rip discs to run them from an emulator for speed, and you're stuck on Linux, then you don't need TurboRip. Something that can rip them to BIN/CUE would be just fine. This cdrdao program is not quite working correctly, but I think the game will load and play just fine. I just wouldn't rely on that image as a backup should your original get damaged or something though.