I'll give it a shot, if only because I'm not sure I fully grasp it either and hopefully I can get some clarity.
Function follows form means to me that how I setup the form, the shape, the structure of a thing will determine how it is used. The best metaphor I can give comes from ceramics, which is my hobby. If I create a bowl, that immediately limits me to using it for bowl-like functions. I can never go back and turn it into a tall cylinder- I have set my course for the outcome of "bowl".
In GTD, this means to me that how I setup my systems will determine how I use them. For example, I choose to process all my email to zero, edit the subject lines with the very next action, and then put them into an Action folder. When I come back to that Action folder to respond to emails, HOW I go about doing it is decided for me- I have a limited number of options, and I can see clearly what the various action steps are so that I can decide what I want to do first. That's an example of a form that's working well for me- it fits it's function.
But if the form does not match the intended function, that's when it's time to make some tweaks to your GTD system.
I'm no expert, but that's my general understanding.