The automatic ball feeder does not come pre-assembled on the pitching machine. It is part of the assembly that you will do after receiving the machine. Therefore, it's just as easy to remove it as it was to attach it.
The Heater Deuce-95 does not chew up real baseballs any more than any other wheeled pitching machine does.
That said, ALL pitching machines with wheels will eventually rip the covers off of real balls. That is because the gap between the wheels is set about a 1/4 inch less than the diameter of the ball so that the ball gets pinched between the wheels before shooting out the other side. Real baseballs have covers that are glued onto them and pitching machines exert significantly more pressure on the ball than a human hand does. Eventually, the tremendous pressure breaks the glue, the covers get soft and then get ripped off by wheels.
If you are going to use real baseballs, please know that they will never be as accurate as dimple balls. Part of that is due to the aerodynamics of a dimpled ball (there's a reason golf balls have dimples on them) but mostly it is because the raised seams catch the wheels differently every time. A real pitcher gets different movement on a pitch by gripping the seams differently so it makes sense that balls will have different spin characteristics leaving a pitching machine when the seams are in a randomly different position and that different spin will result in pitches not being as accurate.
Finally, as it says in the owner's manual, if you are going to use real balls, only use the highest quality leather balls. Synthetic balls or balls with a protective coating will not pitch accurately and will also leave a residue on the wheels, making it difficult to impossible for them to grip other balls after repeated use.