The problem with an interferometer having just two widely-separated points is that it only provides high angular resolution along the axis between those points. (It's not useless, but it is very limited.) The two sites are about 10,000 km apart, which somewhat limits the amount of sky that both sites will be able to see simultaneously (and observe continuously for any extended period of time). If a large number of telescopes are involved in the interferometer array, one needs some very high bandwidth data connections, which I'm not certain exist between South Africa and Australia. In practice, I suspect that what you'd be getting would be more like two Half-Kilometer-Arrays rather than a long-baseline SKA.
What has been proposed, and should be technically feasible, is dividing the array up by frequency band. The plan already calls for three overlapping arrays of different types of telescopes in order to capture three different frequency bands. (Phased array dipole antennas work great at 100 MHz, whereas you need dishes for 10 GHz.) In principle, one could put the low- and mid-frequency arrays on one site and the high-frequency arrays on another. That avoids the problems with bandwidth associated with long-baseline interferometry, and it allows each array to scan its entire local sky without worrying about what's over the distant station's horizon.
The downside is that this increases overall costs. Two sites need to be prepared; two sets of computing facilities need to be built; two different national governments have to be placated. Scientifically, it means that the entire array can't always be 'pointed' in the same place across its entire frequency spectrum--sometimes the high- or low-frequency portion of the array will be below the horizon.
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