The holes I drilled were small enough so the seeds did not go through. I did run into some puddling issues since I drilled holes instead of slats. I made more holes, closer together, to solve that.
However it was not to be. I still had to keep at least one clay box for the one cat, and as long as there was one clay box, they all chose that one over the seed boxes, though they would use the seed boxes once in a while. The one cat who couldn't adjust is my FUTD kitty, and she is also The Litter Box Police. It was just causing her too much stress.
And I was so hopeful....!