Since posting I have scoured the web and discovered a couple of users who have experienced dust build-up in their chassis due to the openings left on either side of the inner dust filter.
With regard to the fan controller, I could only find one user who claims that you have to set the fan speed each time you boot up your system if your preference differs from the default.
As a result I have returned my chassis and exchanged it for the F31, which I believe provides better dust protection. With the money I saved I bought three quality 140mm case fans since the stock cooling on the F31 is inferior to the F51. In lieu of the fan controller I will attach the case fans to my Asus motherboard's fan headers and control it via software.