Gon is shown too tough for his age. In the case of Killua, it is understandable as Killua has undergone a lot of physical torture but in case of Gon it doesn't make much sense or is there a reason behind it?
It may be to highlight the fact that he grew up in the mountains where everything he did was a form of training he did unknowingly. This could explain his insane stamina, speed and perception of the environment, all before he learned to open the gate, or learn nen.
Other that that, I guess you could say it's some genetic benefit? Because his father was the only other person in the entire island who single-handedly caught the giant fish, and at the age of 7 no less! Besides it may also be the quirk of someone with enhancement type nen.
Gon lived in whale island, which was noted for having a wide variety of creatures. Gon lived like a wolf child, despite having his aunt and older relative to live with. Due to his lifestyle, he gained highly enhanced senses, physical strength, and creature like reflexes.
In comparison, Killua was trained from birth, and has have the much more taxing training. Giving him the more polished skill sets and attributes, akin of a proper transmuter. Gon, however, is the more natural of the two, and is by far the more instinctive, truly an enhancer type.
This has been answered in the anime. The island where Gon lived full with wild animals. So, since he was just a little kid, he was fighting them and hunting to get food. For that, he got strong because he was able to train his muscles everyday.
It is actually real. In my country, people who do live for example in the mountains, they are so strong because they eat natural food and do physical activities all the time, lift heavy things all the time, woods, rocks...
I'm not sure the premise of the question is correct, depending on what precisely is meant by "so tough". Starting out and through the end of the Hunter Exam arc, we observe attributes of:
- a high degree of athleticism
- high stamina
- above average senses
- ability to hold his breath for a long time
- fearlessness, and selflessness in regards to his friends and many strangers
- ability to comprehend that birds are worried about upcoming storm
- ability to conceal his aura from Hisoka (natural Zetsu)
- ability to heal quickly, maybe 30% faster than most people
The first five seem well within the norm of a young, highly active 12 year old who grew up in the wilderness. If you don't stretch the bird understanding of #6, it could have just been him realizing they were worried about something, and at sea, that would most likely be a big storm. He was also smelling the storm, probably due to slightly elevated levels of ozone.
Number 7 is a stretch, at least in our universe. Zetsu doesn't exist, so we just have to accept on faith that the development of Zetsu by wild animals is a normal occurrence in the HxH universe. The same goes for the fast healing in #8 -- it is not "real" in our world, but in the HxH world it can be seen as very good DNA.
One scene does seem to demonstrate strength beyond "highly athletic". At the end of the Exam Arc, Gon wakes up with his broken arm, learns what happened, and approaches Illumi with great anger. He even uses his one good arm to lift Illumi above his head and break his arm through force of grip alone. I think he could do this for two reasons. First, his athleticism was being amplified by anger, boosting his strength. This is a recognized phenomenon in our world, see the Scientific American article When Fear Makes Us Superhuman. Also note that Illumi offered no resistance. I think this was due to a combination of honest surprise and curiosity, a recognition that Gon was not a mortal threat, and the knowledge that Hisoka had already claimed Gon as his prey.
I therefor don't think Gon started out unnaturally tough. He had a lot of good qualities from the beginning, including genetics and his friendly, outgoing demeanor. These were not mystical or beyond understanding. After the Hunter Exam arc, he does begin ongoing and consistent training and expansion of his abilities, so by the time he got to Heaven's Arena it would be fair to call him extremely tough and getting tougher every day.