Does this output signal really need the pull up?
Yes, IRQ_REQ output signal requires 2-10K ohm pull-up
According to the section 20.10 of 8548EEC, SD_REF_CLK/SD_REF_CLK_B must be connected to GND if not used. Is this still required even when they have internal 50 ohm termination to GND?
This note is per specfication. Yes, the SD_REF_CLK/_B are 50ohm terminated to ground. They are also AC coupled to the inputs of a differential amplifier. If they are not used and unconnected, we don't want them responding to any differential noise that might be present in the system, hence drawing unwanted current. Thus we recommend tying them to ground so that the inputs cannot respond to any differential noise.
What is the pin compatibility difference between MPC8543 and MPC8548?
MPC8543 and MPC8548 are built on same die and are pin compatible, only reduced functionality in MPC8543E.