It seems to me that the presuppositionalist apologetic is a disgruntled reaction rather than an honest position: someone noticed that debates between Christians and atheists often "presupposed" the criteria for determining "valid knowledge" that are common to the modern scientific worldview, and then said, "Hey, why do that? I can presuppose my own criteria, start from there, and demand that others accept those presuppositions or admit that they've 'lost already.'" After all, Christianity cannot pass the truth tests of "science" since it is not science. The reaction has been to turn the tables, essentially re-asserting the much maligned bumper sticker sentiment, "The Bible says it, I believe it, and that settles it" -- hopefully in a more sophisticated way.
A problem here is a failure to differentiate non-reducible types of validity claims, either through ignoring or discrediting alternative modes, or "subjugating" one mode to another. Atheistic materialism has tended to emphasize empirical observation, concerning itself primarily with objective truth (correspondence, representation, propositional) and functional fit (systems theory, structural-functionalism, etc), and largely ignoring or devaluing subjective experience. Religious traditions have largely emphasized more interior (subjective) value claims and methods of validation, particularly truthfulness (sincerity, integrity, trustworthiness) and justness (cultural fit, mutual understanding,
rightness or righteousness).
These four different approaches are not really reducible to the terms of whatever method one happens to prefer, though society has been fragmented by the efforts of one camp or another trying to discredit other approaches, or to subjugate them to the "ultimate criteria" of its preferred method. I think this is what is going on here in this "reaction" of presuppositionalism (a form of narrow absolutism) to the equally narrow absolutism of the atheist materialists with which many Christians have been wrestling.
