Yeah, hard to see how there could be an instinct (in any useful definition of the term) for a heavily rule-regulated game like baseball. I think the "feel," "knack," etc. for a sport arises from early inculcation and many years of repetition, coaching, and emulation. Even "tools," though necessary and closer to what one might consider innate abilities, can't provide that. In fact, I think that there are just as many times that a "hunch" (the closest I can come at the moment to defining instinct) leads to bad results as good ones, e.g. trying to take an extra base or steal one at the wrong time or in the wrong game situation or all sorts of guesses, such as what type of pitch will be thrown or where a ball is going to be hit, when not based in study or prep. Sometimes a manager's role is to rein in what the player's "instinct" is, such as when a pitcher is convinced they can go longer, but actually should be taken out.