Black onion rot is a fungal disease - you have a couple of options. If you're starting with onion sets, then I'd give a good sprinkle of corn gluten meal on the ground where you're going to plant them, stir it into the surface a bit, then put in the sets. You can't use the corn gluten meal when planting seeds because it tends to prevent germination. That's why it's a good one to apply to prevent winter weeds, and to put down when putting on the soil around bedding plants to slow weed growth around them as the season starts.

Hydrogen peroxide (the store strength 3% variety) is a good fungicide, but even at that strength it will burn the plants. You might want to spray it on the soil the day before you plant onion sets and see if that helps, then add a little to a mix so it's dilute if you ever do foliar feeding in the garden. And you could continue to sprinkle corn meal (cheaper) or corn gluten meal around your onion bed every so often as they grow. Or put corn meal in water to soak for a while then spray the "tea" directly on the plants. You might even want to try spritzing the seeds with a mix of compost tea and hydrogen peroxide before you plant (place them in the ground still moist).

Another anti-fungal treatment is potassium bicarbonate or even baking soda (bicarbonate of soda), a couple of tablespoons dissolved in a gallon of water with whatever else you're putting on the garden - compost tea, liquid organic fertilizer, etc.

It sounds like you could treat the soil ahead, treat the soil at planting and during the growth season.

The only things I don't put in my compost are plants with seeds that I absolutely don't want sprouting as volunteers around the edge. So I get rid of the datura from the front yard flower bed into the trash, the seeds can scatter everywhere and if the dogs eat them it will make them sick.