Yes... long-time Internet atheists are quite familiar with presuppositionalism at this point, since Christian apologists on the Internet have been using it intensively for more than ten years. We've been round and round that bend, my friend...
Here is an old article I wrote on the subject:http://www.strongatheism.net/library/against/why_presuppositionalism_is_wrong/
In another article linked to it, I explain why presuppositionalists "cut their own head," epistemically speaking.
To explain this very briefly, presuppositionalism is basically one huge argument from incredulity. The basic form goes something like this:
(1) Look at logic/reason/the laws of nature/morality/ethics/free will/thought/truth (basically any feature of human understanding).
(2) How could this arise under a materialist universe? I can't see how it could.
(3) So I guess materialism can't explain it.
(4) Therefore God did it.
Their preferred formulation is that atheism or materialism "can't account for" these features. Why not? Blank. What about these materialistic theories that do explain it? Blank. How do you know the Christian God did it? Blank. Where in the Bible are these features ever seriously discussed or valued? Blank.
To hear Sye Ten Bruggencate be seriously debated by atheists, I recommend you listen to episode 15 of the podcast Fundamentally Flawed:http://fundamentally-flawed.com/pods/?p=archive&cat=podcasts
(as a followup, they had me on their podcast on episode 25, which was nice)