Not exactly.
The Per-Player Rake is taken out of the buy-in immediately, before any of it reaches the prize pool, so to speak. Then the Fixed Rake, on the other hand, is taken from the prize pool.
If you set the Buy-in to 55, and the Per-Player Rake to 5, and the Fixed Rake to 5%, then for each player that buys-in, 50 goes to the prize pool, and 5 goes to the rake. That 5 that goes to the rake never goes to the prize pool, so the 5% for the Fixed Rake will be from the prize pool (or the 50 from each player).
If you have 100 players, you'll have 5000 in the prize pool initially, and 500 raked from the Per Player rake. The Fixed Rake will then calculate 5% of 5000 (the prize pool), which will be 250. You'll end up with:
Original prize pool: 5000 (50 X 100)
Per-Player Rake: 500 (5 X 100)
Fixed Rake: 250 (5000 X .05)
Final Prize pool: 4750 (5000 - 250)
I think you've discovered a bug - but I'll need to go back and review this before deciding. It looks like the Fixed Rake, when set to a %, would calculate the fixed rake based on the total Take In (which is 5500, or 100 X 55). I don't think this is correct, since it would be raking the prize pool PLUS the per-player rake. Fixed rake was always supposed to come straight from the prize pool. It's a little difficult for me to tell what exactly is going on since I'm right in the middle of developing other features and lots of stuff is "broken" at the moment...