If I am getting it right, once you assign any amount of energy to an upgrade card you immediately gain two energy.

If you assign only 1 energy to a hardpoint that can take up to two energy, can you assign one more energy to it immediately after you gain the energy from optimized generators, or does in have to be allocated on a different card?

There's nothing in the "allocate energy" step that says you can only allocate energy to a given card once, so I think it'd be a bit harsh to stop you doing it.