The rear element lens sees everything you can see when you look up in the bellows with the lens off. The 'theoretical problem' here is flare on that rear element. You can just ignore it as it is highly unlikely to cause any effect in printing (unless one has a foggy lens). In addition to Ian's suggestion, if one wanted to eliminate any chance of flare on that rear element one could also rig a compendium shade over the rear element. But nobody does this, no manufacture recommends this and it is not needed. I'd spend my time making sure the enlarger is aligned. Enlarger alignment is an art that can take some skill to perfect.
Originally Posted by Ian C