Find articles that validate the similarities between liver and neuronal mitochondria.

I agree with the referee. Liver mitochondria are quite different from CNS mitochondria. For example, they swell and burst during apoptosis. Mitochondria in neurons don't.

I agree with the referee and with James Franklin. In addition I would add that in order for drugs to reach brain mitochondria, they must cross the Brain Blood Barrier (BBB). That sometimes poses a challenge for drug delivery even if the effects are seen in the liver.

Presumably, you mean neuroprotection from ischemic injury, i.e, reperfusion injury. At least WRT oxidative-stress-mediated damage, there tends to be a lot of overlap. That is, an agent that protects liver and kidney and heart tends also to protect brain.

This is true in experimental animals. Neuroprotection studies tend not to replicate in human trials, arguaby because humans are loaded with antioxidant systems such as uric acid that are at much lower levels in the animal models, except for birds. Also, some at least of the damage may be mediated in the vascular endothelium. And some antioxidant neuroprotectants such as urate may work on redox-sensitive glutamate uptake.

superficially one might think that because mito are distinct organelles with their own dna, that they should be the same in each tissue, but I agree with the reviewer. Fundamentally they maybe similar, but not all mitochondrial proteins are generated by mito dna- some come from nuclear dna and so there may be different proteins expressed in mito in different tissues.

The Mitchondrial Pore transition potential is distinct in different tissues, and is a feature critical in ischemia, making liver mito poor descriptors of CNS ischemia. On the bright side your data may be pertinant to hepatic ischemia

If you think of the distinct roles of the cells, in neurite growth and maintaining ion gradients in neurons, or in liver NADPH synthesis for metabolism, Beta oxidation of lipids etc, it is not automatic that one would expect the same environment for each.

As another commenter noted, the antioxidative environment would be quite different- the glutathione balance is different not to mention the PUFA concentration.