I have found a work around for the issue: The compiler is set for mingGW-64
added the following line anywhere to the mbd_s32k.tmf template makefile before opening the simulink model
(located: AppData\Roaming\MathWorks\MATLAB Add-Ons\Toolboxes\NXP_MBDToolbox_S32K1xx\mbdtbx_s32k)
TOOLCHAIN_NAME= "MinGW64 | gmake (64-bit Windows)"
This allows simulink to step beyond some checks when opening the model and then opens the hardware tab,
However, you cannot build the model with this macro in the template file as the following errors will occur:

It is unclear for me why this issues occur, but looking at the implementation of S32k3xx a solution is already found.
However, if you now simply remove the macro from the template makefile again before building but after selecting external mode according steps in Unable to Deploy and Start External Mode Example for S32K144 in MBDT
Then everything worked fine for external mode in 2021b.
Perhaps someone can actually find a better workaround then this, but at least this way external mode is working.
Note that if you change simulink to use external mode then the serial transport layer changes to:

If you then turn external mode off and want to use Freemaster, this transport layer has to be reset to:

The only way I found to do this, is to switch the system target file under code generation settings to mbd_s32k14.tlc and then back to mbd_s32k.tlc. However, this also then allows Freemaster to work again.
Hopefully, these solutions help someone dealing with the same issues.