I would not automate watering of seedlings and clones in RW cubes. That job is best done by hand. It would be very difficult to precisely apply the amount of water needed to dampen yet not saturate the cubes.
If you use 40mm plastic wrapped cubes instead of 25mm cubes, they will hold enough water to get a seedling or clone (before setting root) through 24 hours on a heat mat on one watering. Once clones set root, their water uptake rises dramatically- they'll need watered at 12h intervals. Cubes full of roots will tolerate being immersed, but before rooting or when housing a just hatched seedling, only need a corner of the cube dipped in a bucket to prevent putting in more water than the small plant will use in 24h.
40mm cubes weigh 5g dry and 20-25g when damp but not saturated, meaning they need 20-25ml of water per 24h. If you can automate a system which can precisely apply 20-25ml to each cube and sense when the cubes are getting too dry as roots pop and increase the water uptake, let me know.
I love to automate mundane op tasks whenever possible. This is one job that I've never found an acceptable substitute for doing it by hand.