GOG has a System Shock: Enhanced Edition, which also includes the original version of the game. I have no idea if that version of the data would work with this version of the engine, though. The engine is for the PowerPC Classic Mac OS version of the game.
IIRC the Mac version doesn't use the original data files, but converted them to use the Mac's resource file format. And judging from a quick look at the source code it doesn't contain support for the original data files.
So: no, you'll have to use the Mac version's data files.
Looks like another bump in the road in getting this thing running on e.g. Linux. It'll be interesting to look at reverse-engineered System Shock file format info, and see if anything but the data-loading functions would need to be changed, to use the more widely-available PC data.
From other comments, the sections in PPC asm and the actual I/O APIs would have to be dealt with too.