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No, only the Cell upgrades increase the number and size of Xenocytes spawned. until you've got a number of Transcentions, it's easiest to let the weak Xenocytes accumulate to 33 and then kill one only, once you've gotten the auto-killer.

You won't need to keep your Neurons in sight if you take only as many upgrades to them as you have Genes. It your Genes grow faster than your Neurons, the Tissues auto-clickers iron out any loss in Cells the Neurons generate.

Can you transcend to reset your stats? That seems like the only possible escape here.

I usually just let the green ones block the arrival of any more advanced ones. If you transcended once, you won't even need a single Neuron before you've reached the auto-killer.