Joe, Actually, I had been thinking along the lines of your first suggestion - two shallow, narrow slots inside the lid. The lid is 5/8 inch thick and the crank sticks out only 1/4 inch, which would still leave the wood 3/8 inch thick.
I had also, briefly, thought about the feasibility of having a metal shop cut the shank of the crank (the part that attaches to the machine), remove 1/4 inch from it, and weld it back together. Probably too expensive. Although there does seem to be a welding seam in the shank, not that that helps. I'd also considered shortening the shank by grinding down the area that fits up against the machine, but taking off 1/4 inch would probably leave it too thin.
Tate