I tried having Harvesting Drones by PneumacticCraft to harvest and plant crops. Onion and cabbage goes fine, but the tomato doesn't. They are just getting ignored

That may be a technical limitation.

Tomato crops don't inherit the CropsBlock class because Quark and other mods override its plucking mechanic with right-click harvesting by default. I haven't checked, but chances are PneumaticCraft drones only check for blocks that inherit CropsBlock, instead of checking the AGE blockstate, which all growable blocks would have (including sweet berries).

Considerations to make Tomato crops a CropsBlock again are underway, but not much I can do right now.

Closing this as it's related to #221.