In all poker games I've played so far, rake is only taken from the pot. So if for example there's a pot of 1k, someone bets 1k, and everyone folds, the rake would be 5% of 1k = 50, and not 5% of 2k.
This matters a lot when you are the biggest stack at the table. If I want to push everyone all-in, but I have 100k more than the other people at the table, shoving allin would guarantee me paying 5k extra in rake for no reason, and optimal play is manually counting out the chips that the second highest chipleader has, then betting exactly that. That's a lot of hassle and I can't do that in 20 seconds, also delays the game for other players.
I think it's more satisfying to move the stacks to the middle too, so current state of the game is a bit unfortunate.