These Funko Pop bases were modeled after the D1, D2, and D3 base models. Each one has the peg positioned at a different position relative to the center of the base. D1 is the closest to the center, D3 is the furthest from the center, and D2 is right in between D1 and D3.
If the peg is slightly undersized, try printing at 102/103% scale.