I wonder if a combination of the two sheet system and your vacuum system could work. With the lower plate having suitable tiny holes and the upper plate changing to match the seed size.

Our problem is that with the smaller seeds we might end up with two or three in each cell because of the thickness of the perspex.

Then we place the assembly over the prepared cell trays and slide the top sheet so the holes line up with the holes in the lower and the seeds drop through.

The upper tray is placed over the lower one, but is offset so the holes don't line up. Seeds are spread over the upper sheet and pushed around till we have one seed in each hole.

The upper sheet is interchangeable and has a grid of holes that are sized to the seed we are planting. We have a range of sheets for different sized seeds.

We use a gravity based system consisting of two sheets of perspex. The top one has a grid of large holes that fit the outline of the cells in our seed trays.

How do you stop the seed going through to the vacuum? is it a tiny hole in the bottom of each "cell" or do you have a filter cloth or something at the bottom? Do you have to have different "cell plates" for each seed size?