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Translations: Gintama 515 (2)
'Natural abilities' was him using his nen, it's just was a completely unpolished one. At that time, all the Ants had their nen baptism and were taught the basics by pitou/colt.
The whole 'is this what nen is' is like Pitou realizing nen was much deeper than he previously assumed. 'Strength/speed is not all'.
Even if the guy knew nen by then it does not make speed hit hatsu. That was never said in the manga at all, if anything it makes sense he would have such speed due to his specie. Learning the basics of nen won't turn speed into a hatsu....