I found a thread where someone else had the exact problem you have.
According to one poster, there is another lensboard that will fit the larger 50mm lens.

"for bigger 35mm film lens (say 4/40, 2.8/50, 2.8/63) you need another lensboard made by meopta - it's not so shallow but it has nearly 52mm internal diameter (and 39mm thread) so these bigger lens will fit inside. try to contact some meopta dealers...."

I looked at another lensboard, larger pix than the one you linked to.
I don't know if this is the same as your lensboard, or if it is the one that the poster was referring to. This one has more vertical sides which "might" fit your EL-Nikkor 50/2.8

Other than a different lensboard, you really do not have an option, you have to use a smaller lens.
- Look for a 50mm lens with a smaller diameter. You may have to drop down to a 50/4 lens, to fit inside the dish.
- Install a 39mm to 25mm reducing adapter into your lens board. Then use a smaller lens with a 25mm mount, like a Schneider Componon. You have to measure the lens mount on the lens, Schneiders come in different size mounts.

gud luk