I think they really wanted to use the Wins-above-replacement model but realised they couldn't apply it without knowing the prior probabilities of victory. I agree completely that training of troops matter, morale matters, food and water matter, terrain matters, the technology available matters just as much (steel vs bronze, longbows vs composite bows, cavalry vs infantry, pikemen vs cavalry, musketmen vs pikemen etc). But they don't have any hard data on any of these so they made a simplistic estimate based on troop numbers. An example where this breaks down is in the Battle of Zama, where Hannibal had a numbers advantage over Scipio (40k to 35k) but not in cavalry (4k to 6k). 2k Doesn't sound like much, but it made the entire difference between a small defeat and a catastrophic end to the entire war.
But there are a couple of other issues with the model
1. This model gives more points for fighting multiple small battles and winning them unconvincingly. Whereas it's obvious that a single crushing victory that completely eliminates an opponent should count for more. By that metric, Alexander's few victories should rank well above Napoleon's multiple small ones.
2. How much of the General's success can be attributed to himself and how much to having able aides? How much did Murat contribute to Napoleon's success, or Antony to Caesar's? Unlike a modern basketball team where you can measure a player's impact by seeing the team with and without them, it is difficult to quantify how much or how little Murat contributed to Napoleon's victories.