Well, three things:
1) They implemented this multiple-harvests option with the intent of making it easier to harvest stuff from mog gardens
2) They left this very obvious hole in it where you stop multiple harvesting when the harvesting point moves
3) If you use fertilizer, you can freeze the harvesting point at one spot

Now, the only reason I can see for them leaving such an obvious hole (fixable with fertilizer) is if individual harvesting point locations (within #4, or #3, and so on) have different drops. So their idea may be that you're supposed to harvest -> harvest -> "Ooh, it's the good point!" -> fertilize -> harvest

Of course, no one really cares about which point gives them the most 3k logs, so no one has bothered to figure this out and they could really do us all a favor and abandon the idea as you proposed. However, that might be what's going on.