But it's not exactly true. His body statistically is not the best for football. In fact he had a growth problem he had to take hormonal treatment for. Initial coaching opportunities are thanks to the parents, but then he had to work hard to qualify for Barcelona youth program. Then he had to move to Spain as young teenager to be able to continue training at the required level. Amount of hard work and sacrifice he invested is way beyond that most other footballers do, and incomparable to normal population at all.
Shorter people have a lower center of gravity which is an advantage for players maneuvering the ball through the midfield. There is certainly a trade off with strength and vision but Messi's body type is hardly unusual in top flight football. Xavi and Iniesta, who played with Messi on Barcelona, were superstars and all three are 5'7".
Messi is 169, average height at the World Cup is 182.4, this is quiet a difference. In fact he is in the lowest percentiles. Ronaldo is 187, Neymar is 175.
why do you care about the average height? - in some positions being taller is better and others being shorter - being an average doesn't mean that it's in any way better.
So he was lucky to go through a system that had him competing against higher level talent while at a physical disadvantage. By far the best way to train at a young age. His statistically good body for football counterparts meanwhile competed at amongst themselves and with lower talent. He was lucky enough to be good enough to push past the barrier of being able to be in a situation of advantageous training. It is a very rare position that often leads to exceptional players.
He also was lucky enough to be born. If you take to absurd, you can attribute anything to luck. A lot of kids where in position like him, and none made it to number one.