Many people dont really get scientific about it and just populate every slot because they think it looks nice. Nothing wrong with that and with that much air flowing through GPU and CPU will surely get enough fresh air too them.
Its not the most efficient way though, especially if like me noise means anything to you.
I dont really understand why three bottom intakes would be counterproductive to the GPU fans. I would imagine the opposite. Considering I have tested cases in multiple configs and a bottom intake and/or side intake onto a GPU has always improved temperature on it. Never tried a case like the Dynamic O11 though. It was designed with watercooling radiators in mind I believe.
The front side intakes on the dynamic can't really provide a lot of direct airflow over the motherboard and components, just a lot of turbulence as it enters and bounces off the side panel. Not optimal for air cooling I imagine. Ideally I would think you'd need air flowing as quickly as possible across and out with as straight a flow as possible, which is why I suggested bottom intake and top exhaust config first.
Of course the problem is that every setup has different components, different rpm/pressure rating for fans, GPU's might have 2x10cm or 3x8cm fans of different sizes and CPU coolers the same thing.
If the case is in a corner where hot air tends to pool then you might find different fan configurations with the same components work better than someone who has their case next to a door or window. All these factors can affect results.
If you really want optimal you'd have to test all yourself with your own setup, you dont need to go that extreme, but you did ask what was optimal