We do? Well, I don't! My personal understanding is that conscientious is a trait which is semi-fixed in personality, but that for most people (people with normal psychology, which is the realm to which Big 5 is applied) it is largely learned behavior, not something that results exclusively out of inborn traits: according to many psychologists, most infants are impulsive and low on conscientiousness, and it a a parent's job to teach conscientiousness. The result is that most people are average in conscientiousness, as they are average on the other 4 dimensions as well.
Socionics, as a theory, holds that each person's type is a result of inborn preferences, not of learned behavior. The effect is that each (healthy) person has a specific type, i.e. is not cross-typed. If you claim that Socionics is basically the same as Big 5, then the theory behind Socionics is invalid, and we can simply discard it. Or top put it differently: If Rationality/Irrationality is the same as Conscientiousness, then Socionics, as a theory, is invalid.
The question is: can a rational person be low on conscientiousness and an irrational person be high on conscientiousness? I think insights of Cognitive-Behavioral Psychology on conscientiousness, impulsiveness and procrastination show us the question can be answered with 'yes'. Low and high conscientiousness (in the pathological sense) can be unlearned (with quite some effort), but I doubt it changes cognitive style.