I asked in the Togepi Mirage/Paradise thread what people thought the mirage/paradise was. Two suggestions were an alternate universe or dimension. So apparently some Pokemon can travel through universe/dimensions. That reminded me of Nightcrawler from X-Men who teleports by going from his dimension into another dimension and coming out at a different spot in his dimension . So could teleport in the Pokemon world work the same way?
There are numerous ways it could work. One is by shunting into a parallel dimension, but the other is the old fashioned mass-shift to a new location (think Star Trek). But maybe Pokemon didn't originate on the world we're shown, and they began by teleporting in, like the place, and stayed. And now when they teleport, they're shifted back home briefly.