Because the ocean basins really are short-lived features on geologic times scale, reconstruction the world’s geography by backtracking along the hot-spot trail works only for the last 5 percent or so of geologic time.
Or so is an idiom that means "approximately". So the author is saying that this method works for approximately five percent of geologic time.
You see this idiom used a lot with numbers where the exact number is unknown or unimportant. For example,