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The effect of the TCB_FLAG_CUSTOM_STACK flag is the the OS will not attempt to free the custom stack memory if the kernel thread exits, crashes, or is killed.  Does this matter in your implementation?  Could this result in some kind of memory leak?  If any kind of clean-up is required by your application to free the custom stack memory, you will probably want to use an on_exit() or atexit() function to get a callback when the kernel thread is terminated.

If TCB_FLAG_CUSTOM_STACK were not set in the TCB flags, the OS would attempt to free the stack using kmm_free() which is probably not what you want in this case.