Timer Interrupt Setup in ThreadX
Ok, so after some more digging around I think we've figured out the answer to this:


Regardless of the Timebase Source setting in CubeMX, HAL initializes the SysTick timer and enables his interrupt in the NVIC.
After ThreadX loads for the first time, it overwrites the values in the NVIC to fit the value of SYSTICK_CYCLES.


This means that basically, when using the function HAL_Delay() it will count the interrupts created with the Timebase Source. When calling tx_thread_sleep(n) the CPU will sleep for n SYSTICK_CYCLES cycles. 

So short answer, there is no immediate connection between SYSTICK_CYCLES and the CPU SysTick. But if you want to use the HAL_Delay() function, make sure that it's set correctly.