Point one: you may think you are stopping at the same point, but you're not. The cylinder is stopping either from its own internal stop or from the external stop, but not from both. Physically impossible.
Point two: There is no "best" stop arrangement for cylinders. That's because some cylinders are moving heavy loads, some aren't. Some move at high speed, some don't. The best stop arrangement depends on the loading and speed, neither of which are described in your original post.
As a general rule (learned over 35 years of experience) I much prefer external to internal stops. The best way to damage a cylinder is to expect it to absorb the high shock loads associated with rapid decelerations of high momentum loads.
Built-in internal cushions can be nice but are usually of limited value if you analyze the details of their operation, especially if the final stopping position is variable at all.
Point three: Another VERY good way to damage a cylinder is to arrange the external stop is such a way that it creates an offset load on the cylinder creating a moment on the cylinder rod and end seals. Either put the stop in line with the axis of the cylinder or install some other means of absorbing the offset load.