Sorry for late reply.
I'd like to know if you mean the INITX can not be driven as low even though the BMC driving output is low? I don't think the internal pull-up can effect the low level output.
This topic gets any update over last months?
It seems caused by the pull-down resistor in your BCM together with the pull-up resistor of MB9BF368N INITX pin. Maybe the drive mode of BCM controller pin is wrong and the pull-down resistor should not be there. Let me know if you already have get this issue resolved.