It seems to me that Twain is actually satirizing adult or "learned" behavior, or perhaps conformity in general. Notice how he treats several topics, such as obedience, deference or respect, and lying. He inserts certain words that betray the stated purpose. For example, he writes, "obey your parents, when they are present," because they "think they know better than you," actually implying that parents do not know more. Regarding respect, he writes, "Respect your superiors, if you have any...," as if to say there may be none superior to you. His discussion of lying is very interesting. He warns youth "to be very careful about lying," or else "you are nearly sure to get caught." He then continues the discussion of how we should not lie until we've grown & learned enough to become "perfect" liars, with "confidence, elegance, and precision." He then continues to further support his theme of the adult world that so admires a "lie well told" that it rewards the liar with profit & accolades. Twain advises youth to start "early" to learn "this gracious and beautiful art...If I had begun earlier, I would have learned how."
One view might be that he is advising youth to prepare to join & be competent in adult life, in which disobedience, disrespect, and lying might be considered survival skills. However, considering that the true purpose of satire is to try & bring change, it is more likely that Twain is satirizing the "do as I say - not as I do" adult world. I believe his comments are actually aimed at adults - not youth. He is probably trying to point out the errors of adult cynicism, with a view toward making society more honest, cooperative, and rational In the long term.