The system is very rarely used to defend Judaism per se. Chavrutas will only very rarely debate or argue over those fundamental premises.

As to your friend- I'm pretty sure he's the exception rather than the rule. Having interacted with a large number of Orthodox Jews (both when I was Orthodox and after), they aren't any better at apologetics than the average Christian. Epistemological issues exist, but they exist as they do in essentially all religious frameworks (I'm actually beginning to think that common epistemological flaws are one of the unifying features of religion). Judaism has some epistemological problems that many forms of Christianity do not have, such as heavy emphasis on tradition and ancestral belief as extremely strong valid evidence, but these problems seem to be divorced from the chavruta system.