Hello @rsating ,
In MBDT we do not offer support for selecting the muxing GPIO settings, just because we don't have such component like PEX, the one that you show in the last screenshot, something like a dedicated pin muxing block.
Instead of that, we check to have each pin assigned to a single peripheral only, and we generate the pins C code initialization with settings for that peripheral. All our peripherals config blocks, have a 'Pins' drop down selection, from which you can select the desired pin and that block will generate assign the Alt mux option directly in C code.
For example, all the hardware CS pins of the SPI blocks, can be assigned from the LPSPI_Config block. The drop down options will be displayed dynamically with options available for the selected instance. If you want to use the PD3 as CS0 for the LPSPI 1, you have to select the PD3 as PCS0.

This will automatically generate in the C code the mux that you are looking for.

For the BMS TPL Communication, we have an article on the Community, https://community.nxp.com/t5/NXP-Model-Based-Design-Tools/BMS-amp-MBDT-MC33771B-MC33772B-TPL-communi... describing the scenario that you are interested in, alongside with example.
Hope this helps,
Marius