It's not true necrotic damage than. If it's not even magic than we have to derive the mechanism. If it is purely mechanical or if it works like poison, or something else it is on the molecular level, stone may still block it.
The natural resistance of the Bulette doesn't stop magic, it doesn't stop poison, it stops normal mechanical damage at a macro level. It grows stoney scales as its body processes ore and stone. A magic can bypass the resistance because it is slightly out of phase with the material plane.
So suppose your nanobots can seep through the scales and attack directly, bypassing the stoney hide, but it's not the kind of thing that resonates with undead magical energies.
However, if it can't effect a magical energy, then in the case of skeletons and zombies, they really don't care if they lose a pound of flesh. They are magic/mechanical constructs.
So if I would rule one step in your favor and in that case it doesn't do anything to the undead at all, but if you added that your hand of healing does nothing to living beings then the hand of harm should be symmetrical and do nothing to undead beings. But if your hand of healing does heal living beings, the hand of harm should still heal undead beings.
In any case, the advantage now is, you can target creatures immune to magic damage. This will come in handy.
Follow this logic, if a creature is immune to necrotic damage, you would be able to harm them normally, but an undead creature, instead of being healed, is now only immune. In this case, I could either just allow it or say they have resistance to it or half damage because if it was normal damage in this case the Bulette would be resistant.
Weighing everything together, I'm going to allow it to act as normal damage for this particular creature, meaning your pseudo necrotic damage will harm it but will be resisted 50%. Fully magical creatures like ghosts or wraiths, it will do nothing.
Your hand of healing is ok as is for normal creatures and will heal magical/mechanical creatures 50%, ethereal beings it will do nothing.
Ashley's summons are in that catagory of 50/50. M3gan is in a sense T1 terminator and you are T2, including her panther form, neither use magic, she is a demigoddess construct evolution of the same technology tree as you are by design.