Hello Ludwig,
I ported MPC5643L PinToggleStationery example for S32 Design Studio, please see attachment in this post. It is not "absolutely amazing", but it works correct ;-).
About your compiling issues, you cannot use startup from CodeWarrior, because it uses different compiler. S32DS uses GCC compiler and for example, there are no pragmas and also as I know there is key word attribute instead of declspec. But these are not only changes.
So please check the example and let me know, if it works on your side.
About MPC5748G I did not test code flashing via USB (there could be some problem with Open SDA firmware, but I guess only), but if you use Multilink it takes about 30 seconds (there is big flash memory).
If you have any other question, please feel free to write me back.
Regards,
Martin