You found the difference in the enlargers for the negative carrier.
Supposedly it was so you could rotate the carrier, and thus image, so you did not have to rotate the easel.
The D5 carrier has another panel screwed to the bottom plate. This panel will sit inside the round cutout on the negative stage to align the carrier. You would have to put at least 3 equally spaced pins on the bottom of the lower carrier to center the carrier in the hole. The trick will be locating where to put the pins.
If you don't care about being able to rotate the carrier, then put the pins into the negative stage of the D4.