The parent comment was referring to mathematical properties of the voting system itself which tend to give rise to a two party system almost automatically (specifically, the combination of a first past the post voting system and single-representative districts)[1]. The Founders were not aware of these effects and could not compensate for them, so their vision of a party-free democracy did not prove relevant to how the system actually functions in practice.

[1]https://en.wikipedia.org/wiki/Duverger%27s_law