I think you meant MCF5485 Reference Manual, its on page 457. I know the pull ups are usually to keep the line high when not in use or for faster switching. The series im not sure about. Perhaps its just to limit the current. I never used that processor so sorry.
These resistors function to correctly terminate the high speed logic lines. Note that the 50 ohm resistor is not pulled to VCC, but it is pulled to Vref. That is an important difference. Here is some literature to help explain: https://www.electro-tech-online.com/custompdfs/2011/07/MT-097.pdf