Yah, It could mean a few things.
A. Time Travel is involved.
B. Another clone was made.
C. He hasn't aged yet, and that was from the very beginning.
D. It was just something random.
The most likely answer is, and I would stake my reputation on it as an MGS fan, is that he was just using his mask to change into the younger image of himself. It is confirmed the mask can do that, so I think that is what happened.... although Option C could also be a possibility, and I think a very cool one.