Oh yeah, I would too. The gal I bought the Silkie eggs from said she builds little separators out of hardware cloth, like 1/2" or 1/4", and covers any sharp edges with masking tape. Like little baskets that sit on the mesh. Also said she lines the bottoms with that rubbery shelf liner, an idea I really like and will use. I had intended to hatch in cartons as you are, but she strongly prefers lying them on their sides, and since she has long success that way, I will do so as well.
Wrote down my viable count, I have 4 Lavender, 3 Porcelain, 2 White, and 1 each Buff and Blue Splash. I originally was going to separate them in the hatcher, and still want to, but it will depend on where I'm at with everything else. Porcelain and White could be really tough (probably impossible) to tell apart at hatch, and even a light Lavender could be really similar. I think I'm almost exactly a week behind you (set at 4:30 am two weeks ago). The rest were not even possible hatches, so they are removed. I would have liked for the two Paints to be viable, but alas they are not. Still not bad. If they hatch. The 11 are all looking good today.