1| You may want to
read through this since you're going on about positive and negative air pressure. I for one am trying to get by with the basic rule of physics whereby hot air travels upwards(hot air is less dense and so moves upwards). In the scenario of a PC case, that hot air will travel out the top and/or the back as they are located at the highest point. Following that, cooler air can only be found lower when compared to heated air this is why I've suggested having a bottom fan mount draw air in. As a followup, the logical area for air to flow through if bottom mounted locations are dust magnets is the front of the chassis.
2| If I were you I'd get all fans in PWM flavor and have them all plugged onto the PWM hub. The PWM hub can then be connected to a PWM fan header on your motherboard, like CPU_OPT, and via BIOS the fans RPM will flux with respect to the CPU's temps or follow a particular fan curve/profile.
3| If you're looking at fan controllers, they don't allow for PWM control but they do offer granular level of control however that sort of thing is meant for people with custom watercooling loops. In fact they control a fan via voltage regulation as opposed to the pulse seen on PWM fans(and their headers). The disadvantage with fan controllers is the cabling mess and that each channel would be populated by one fan. If you add splitters per channel you can and will reduce the longevity of the fan controller. You need to understand that a fan controller operates by reducing the amount of power delivered to a fan. That reduced power translates to heat off
a resistor which is the heart of any fan controller.
I don't understand why you'd want to spend more than twice the money over a PWM hub and get a physical fan controller...?
On second thoughts, mind sharing the rest of your (proposed)build?