2. Explain what is wrong with
the example (the one with real numbers) that shows the reward per block is smaller for big miners.
Right here;
Reward per block for 1% miner: 5943 * 0.0006885 + 3.2223 - 0.4589 = 6.8552 BTC (more than in scenario 1)
Reward per block for 90% miner: 7251 * 0.0006885 + 3.2223 - 3.5294 = 4.68521 BTC (less than 1% miners in this scenario; more than the miners in scenario 1).
No miner is going to mine a block that costs him more than 2 BTC to mine. Since it's not economically viable to mine larger blocks, you're right that there isn't an economic advantage given to the larger mining entity, and what I wrote earlier wouldn't apply. What I wrote would only apply to penalties that don't reduce the reward below the target block size reward.
Why would a miner mine a block at a loss just to accept more transactions? Regardless, any market participant that engaged in this behavior would just get out-competed by another that didn't.