Not a stupid assumption at all. Sometimes the opposite of a recessed board is necessary. I have an Omega D5XL with the three lens turrent. One of my lenses is the older-style Schneider 100mm f/5.6 Componon-S. It has a rear element that protrudes sufficiently such that an extended lensboard is needed to allow the turret to rotate freely. Focus is achieved by simply racking the bellows a bit higher. It all depends on your particular enlarger hardware limitations.
If your 50mm won't fit into the recessed board, perhaps you could trade it for an earlier Componon-S without the arm? I prefer this type myself and use a matched set of 50, 100, and 150mm Componon-S samples from the mid-80s. None of them have arms. (Or those annoying lighted aperture scales.)
Or maybe you could even find a way to shift the bellows upward just enough to bring the lens closer to the negative? I'm not familiar with your enlarger, but perhaps it's worth a look?
Ken