Hi Stefan,
which version of S32 Design Studio you use? Version 1.0 or version 1.1?
I have already tried the project you shared (https://community.nxp.com/servlet/JiveServlet/download/11363-386434-629570-376197/mpc5748g-ethernet-... ) and I am able to compile in S32 Design Studio. Only problem was with with path include in system path. Instead of include there was some another absolute path, which causes error during compilation.

Maybe there is similar problem in your case. Try to look for project paths and change absolute paths to relative ones.
Especially, if you have another path to S32DS installation folder than C:/Freescale/S32_v1.0...etc, you have to change this include to correct path. Also if you have S32DS version 1.1, path to e200_ewl2 will be little different. So please check and let me now if this was the issue.
Regards,
Martin