Hello @StephP,
First of all, i want to mention that the MBDT for S32K1 has been release in 2022 and it has been only tested on the MATLAB & Simulink versions from R2016a to R2022a, which were available on the release date. Unfortunately, there is currently no release planned to address the R2025b. However, I have tried to run the same example on my end on R2025b and it generated the .elf file.
Now, I had a look on your log, and I have some suggestions you might try.
1. Try deleting the gpio_s32k144_mbd_rtw folder, together with the slprj folder and try generating code again.
2. Try uninstalling and installing the toolbox in a shorter path with no spaces and then try again. You can do that by adjusting first the MATLAB Add-Ons Settings under the Intallation Folder in Settings -> MATLAB -> Add-Ons.

Hope this helps,
Marius