How do I get an IBM thinkcenter A50 to see a CD drive in boot order?

Typically if the PC cannot 'see' the physical hardware, it won't let you enable it in BIOS.

I would unplug/reseat the drive, maybe whack it gently, and see if the drive door opens when you press the button and/or there is evidence that the motor is spinning.

Sometimes it helps to do a 'reset to default' for BIOS settings.