A4000T rear card

[X-ray]

Jeff is right.
Another user here (I can't remember who) cut that board so that the terminator was free, thus enabling the use of the little D-sub cutting in the case (which was previously obscured). That's nice if you have a non-zorro graphics card for instance.

[X-ray]

@ Will-I-Am

The cuttings at the back of the case that are obstructed, are the same size as a PC VGA port, so if you had for instance a CybervisionPPC in your A4KT, you could run the output to that opening if the SCSI terminator part of the ports module wasn't in the way.
The black connector (the 50 pin one on the ports module) is where you would plug the last connector on a SCSI ribbon cable, for termination. So you would have a setup like this:

50 pin connector on disks module ------> SCSI HD --------> 50 pin connector on ports module.

That is with one device and with a ribbon cable with 3 connectors. In other words it is a terminator for internal SCSI devices that are on a 50-pin ribbon.