Hello,
Sorry for late reply, this thread hasn't been assigned correctly somehow.
This is an issue relating to the integrator itself rather than a RTD driver issue. The reason is quite complicated, however I will try to explain as simplest as it can. After configured all the stuff, the following arxml file will be generated in DaVinci:

This file will be used as an input for a generation tool. As you can see, the order of the peripheral is McuPeripheral_0,1,10,100…, but the generation tool expect an order like McuPeripheral_0,1,2… As a result, the generated code will not matched with the configured values.
Please follow the below steps as workaround:
1. Start from EB Tresos, you create a project with S32K3xx platform and configure all of the MCU peripherals, enable the peripheral clocks that you want to use.

2. Change the Name field of the peripheral as below:

3. Export the project to arxml file, by Right click to the project -> select Im – and Exporters…. An Importer/Exporter window will be shown. Press the Plus button (the green one) to add a new im/exporter object. Select Export Only then press Next

4. Fill the exported arxml file with full path, select the AUTOSAR version (4.4.0), then Finish. After that, press Run Exporter to get the exported arxml file

5. Import the generated arxml file to DaVinci tool.
Hope it helps and sorry for any inconvenience.
Best Regards,
Nam