So,
I found the error myself. It seems that the Keil projects for (at least) the BM versions of the MTP samples misses a "define" in the linker settings.
The FreeRTOS version of the MTP sample has the following set in "misc controls" in the linker settings:
--remove --predefine="-DXIP_BOOT_HEADER_ENABLE=1" --predefine="-D__stack_size__=0x2000" --predefine="-D__heap_size__=0x2000"
The BM (baremetal) versions of the MTP samples only have this set:
--remove --predefine="-D__stack_size__=0x2000"
This means that the scatterfile will not work correctly when placing code in FlexSPI/NOR Flash:

I updated the bare-metal versions of the MTP samples and they now also run perfectly
Maybe it is worth for NXP to check all the samples if the same error has been sneaking into some other samples