Of course playing the way you've played for years is going to feel more "natural". But that's the wrong word. The word you're looking for is habitual. Anytime we alter our familiar postures or movement patterns it seems uncomfortable at first. Even people with terrible - potentially damaging - posture will claim that standing with a straight back and relaxing their shoulders feels "weird" and "unnatural". Our bodies/brains simply become accustomed to our habitual poses. This, by no means, suggests they are "natural" or even beneficial.
That's a different question. Sometimes the most subtle things can cause adjustments elsewhere in the grip and stroke and lead to inefficiencies. That said, there are several schools of thought on the pinky. While Tommy Igoe might say that "pinky gets a free ride", Jim Chapin or Tony Williams or Jojo Mayer would disagree.
My thinking is this: it's there, why not let it help us? It can be VERY useful for certain finger-based techniques, and is also very useful for gripping the stick in the Swiss/Moeller/Williams style - a grip which provides a lot of power as well as a near-direct transfer of force from wrist to stick. Note that when you grip the stick with the last two fingers on it, any movement of the wrist leads to motion of the stick without delay. This may, or may not, be advantageous to you.
You mention it being under or over your ring finger depending on the hand. For starters, unless your hands are different - and assuming you play matched grip - wouldn't it make sense to construct your grip in the same way for both hands? Moreover, if the pinky is over the third finger, it suggest to me that it is out of its normal, relaxed alignment with the hand, meaning that there are muscles and tendons engaged somewhere which may not need to be -- depending on your hands, of course.