It still has the tradeoff of making travel close to the center take longer than it should on a sphere (worked around by limiting diggable height), but i find it a more elegant solution.
One example of this: I would expect each location would not have a single antipode (opposite coordinate) but would instead have three. If you were to start at location A, rotate travel 180 degrees along the latitudinal axis to location B, then 180 degrees around the longitudinal axis... on a sphere you would expect to be back at location A, albeit upside down. But on a torus, you are in a completely different location, which is the 'C' antipode. Rotating 180 degrees latitudinally from here will bring you to point D, the last of the antipode set.
One of the worlds i played on had road planning from the start and a set of roadways covering the entire world in a 4x4 square grid. Pathing to point D was just a matter of going 2 blocks in one direction, and 2 blocks in an orthogonal to it.
In a world without such roadways, you'd look for landmarks such as oceans and continents instead.
Ultimately, you don't care if somewhere is antipodal or not because you never see the antipodes to where the globe is currently looking at without rotating the globe.