I seem to have confused you with all these thoughts. I never compared rake to the players' stacks (only with the "money" entering the pots). I tried to estimate how much the tournament rake would be, if (hypothetically) it was held with cash game terms, i.e. if every time a pot was won (with the flop seen) the dealer would hold some of the tournament chips of the pot as house rake. Finally, the winner of the tournament would cash out his prize based on the total number of tournament chips left. The rest of the prize pool would have been the tournament rake (but held with cash game terms). And if it weren't a winner take all tournament, then the rest of the players would be paid according to the percentage of the final prize pool (after subtracting the rake from the buy-ins) that corresponds to their finish position. I will give you some numbers to make it more clear:

Imagine a tournament that starts with 10 players, $10 buy-in and 1000 chips initial stack. Each chip is worth $0.01. Let's say first one wins 50% of the prize pool, 2nd 30%, 3rd 20%. But that's a tournament that the rake is held in chips out of every pot, when players see a flop. So, let's say that after the end of the tournament, the winner accumulates 8000 chips (because the rest of them were held as rake by the dealer). These chips are worth $80, so the winner will cash out $40, 2nd place will cash out $24 and 3rd player $16. So, the rake of such a tournament would then be $20 out of a total of $100 (sum of buy-ins), so it is 20% of the total buy-ins. In this tournament the rake was held with cash game terms.

What I am trying to prove in my article, based on the numbers I have run, is that if there was a way to hold the rake of tournaments in the way I just described above, they would be much more expensive than they are now that we pay the rake in advance, as a certain percentage of the total buy-in, no matter how much "money" (chips) enter the pots we play, how many chips change hands without a flop seen etc. This way, I tried to prove that a certain edge a player has over his opponents can be more easily exploited in tournaments, because the rake becomes more beatable the way it is paid, in comparison to the cash games. I think this also proves why cash games have become more difficult nowadays, as well as turbo tournaments are harder to beat than regular speed ones. Some poker rooms also give players motives to play turbo SnGos by charging a smaller percentage of the total buy-in as a fee.

I hope I made it clear now

I wish you have a great weekend too!