Hello @monchito911
The first suggestion I would have, related to the information you have detailed in this thread, would be to migrate your setup to the latest MBDT for S32K3 v1.6.0 - which was released at the end of January. The latest toolbox version will allow you to benefit of the latest framework improvements we have made, and also access the enhanced set of peripherals, drivers, and application examples that we deliver.
Now, for addressing your specific encountered issue, I would like to mention the following:
As far as I can see from the NXP website, the T-Box comes with an S32K344-Q172 processor, so I am not completely sure if this is the board that you have, and if the Q172 package is the one targeted by your hardware setup.

Inside the MBDT for S32K3 1.6.0, the Hardware Part is populated by default, based on the selection of a Default Configuration Template - this represents a configuration project, enabling the peripherals, pins, and clocks, that targets the processor you are aiming to use. Selecting such a Default Configuration Template will enable you to use this configuration with the application you are developing.

This default configuration is designed to address, in the case of the S32K344-Q172 processor, a different evaluation board, more specifically the S32K3x4-Q172 (https://www.nxp.com/design/design-center/development-boards-and-designs/S32K3X4EVB-Q172). Hence, all the settings, pins routing, and peripheral instances enablement are not enabled to match the hardware configurations of the S32K3 T-Box.
However, this does not provide any limitations, as we indeed enable the option of creating custom hardware configurations, to address hardware designs that we are not providing out-of-the-box support for (like the case of S32K3 T-Box), and the process to be followed for manipulating such custom templates is in details described inside the Release Notes document delivered together with our toolbox - please check Chapter 3.6 Support for Custom Default Project.
For creating such a Custom Configuration, you could start from the default one we provide for the processor you are targeting.
For creating such a configuration, for a specific hardware board, indeed you might need to change the pins routing (according to the board's schematic). A detailed guide covering how to create a DIO configuration for manipulating I/Os on a custom hardware is available here, in this article we have posted on the MBDT Community.
To conclude:
You would need to create your own configuration for the S32K3 T-Box, following the processes described in the Release Notes referenced chapter + the article demonstrating DIO configuration.
As a personal recommendation, I would start by creating a Custom Project Template starting from the one provided as default for the S32K344-Q172 processor, and save it somewhere separately. Then, based on the steps described in the article, I would modify it to match the T-Box. After the configuration is completed, I would use this new file as the Configuration Project Template for my model, and try and run it on the target.
Please let us know if the provided references are useful for your use case, if you encounter any issues in following these workflows, or if more information is required from our side.
Thank you,
Irina