There are a few things I dispute.
For the negative pressure case:
Amplification of natural convection
While the top fan blowing upward does indeed support (rather than oppose) natural convection, this is not a trait of a negative pressure setup. This is a trait of proper fan orientation (cover in the last article).
Negative pressure means
fewer particles available to transfer heat to. Thus negative pressure
opposes natural convection. Conversely,
positive pressure with a
more particles available to transfer heat to
supports natural convection. A good example of a properly oriented positive pressure system is the Silverstone Raven 2/ Fortress FT02.
Compatible with all direct heat exhaust graphics cards (the ones that blow dissipated heat out of a vent built into the shroud)
Again, the more of a vacuum you create, the fewer the particles available, the worse the heat transfer. As a side note, fans are noisier in a vacuum as well, but I'll let you look into that if you're interested. In the setup your have, orienting the top fan downward would suck in some of the exhausted heat back into the case, but that again is a fan orientation issue. Again, the cases mentioned above post some of the best video card temps in the industry (especially for external exhaust style cards).
Augments the cooling performance of downward-facing CPU heat sink fans
You'll have to explain this one to me, but I suspect this is another fan orientation issue rather than a positive vs negative airflow issue.
Without a dust filter, dust gathers inside the case
Even with a dust filter, you have to understand that most cases aren't air tight. With negative pressure air will be drawn in through every crack, bringing dust with it.
For the positive pressure case:
Only average cooling performance in enthusiast-oriented configurations
There are many counter examples to this statement. I'll stick with the Silverstone Raven 2/Fortress FT02. Though I do agree that if you orient the top fan down in the example case to achieve positive pressure, the improper orientation with drop your cooling effectiveness.
Better support for graphics cards without the ability to exhaust dissipated heat
Not sure this is true either. While you do have more particles to work with, negative pressure systems tend to be better at directing airflow. This makes it easier to direct the heat away from the video card and out of the case. Of course, their are positive pressure systems that can achieve this as well.
Only with an inappropriately oriented fan such as in the example you show. Not an inherent flaw of positive pressure systems.
Air flow is determined by size/position of case openings
Having a hard time seeing this as a negative to positive pressure systems. This allows you to put the air where it is needed. I tend to think of a negative pressure systems more intuitive ability to direct airflow as a positive. If anything, it just requires more thought. At the opposite extreme, highly negative pressure systems can suffer from air coming in holes in the case and going straight out without doing any effective cooling.
Counteracts the cooling performance of downward-facing processor coolers
Again, you'll have to explain this one, though I suspect it is an orientation rather than pressure issue.
Graphics cards with DHE (direct heat exhaust) can partly counter the overpressure
This is true, but can't be considered a downside to cooling, especially when you already think the positive pressure systems don't cool as well. Rather it is something to consider (along with the PSU) as you design your cooling system.
A true downside to positive pressure systems is that you can get areas where air simply stagnates and doesn't get drawn into the flow. This leaves you only marginally better off than straight convection cooling. A good positive pressure case will make sure that air is still flowing around the components that generate heat.
In my findings, the best results come from a slightly positive pressure case. These still benefit from being able to direct the airflow for optimum cooling, while preventing dust build up and removing the vacuum effect. Though I must admit, the Silverstone Raven series/Fortress FT02 cases seem to get around these issues while remaining highly positive pressure. That said,
fan orientation is of far greater concern, and should be setup to direct heat out of the case smoothly as shown in your first article. Improperly oriented fans will far outweigh the benefits of positive/negative pressure systems. In other words,
make sure the case is designed for the type of system you want to implement rather than forcing the system you want on a case that isn't designed for it.